BMRB Entry 25562

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25562
MolProbity Validation Chart

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Title:
Structure of the PR domain from PRDM16
Deposition date:
2015-04-02
Original release date:
2016-07-05
Authors:
Sun, Yizhi; Armstrong, Geoffrey; Briknarova, Klara
Citation:

Citation: Sun, Yizhi; Armstrong, Geoffrey; Briknarova, Klara. "Structure of the PR Domain from PRDM16"  .

Assembly members:

Assembly members:
entity, polymer, 176 residues, 19169.670 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pDEST 15

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSGFPTSEDFTPKEGSPYEA PVYIPEDIPIPADFELRESS IPGAGLGVWAKRKMEAGERL GPCVVVPRAAAKETDFGWEQ ILTDVEVSPQEGCITKISED LGSEKFCVDANQAGAGSWLK YIRVACSCDDQNLTMCQISE QIYYKVIKDIEPGEELLVHV KEGVYPLGTVPPGLDE

Data sets:
Data typeCount
13C chemical shifts737
15N chemical shifts168
1H chemical shifts1160

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 176 residues - 19169.670 Da.

The recombinant protein contains three extraneous amino acids at the N-terminus and residues 54-226 of human MEL1 (gsgFPTS...GLDE).

1   GLYSERGLYPHEPROTHRSERGLUASPPHE
2   THRPROLYSGLUGLYSERPROTYRGLUALA
3   PROVALTYRILEPROGLUASPILEPROILE
4   PROALAASPPHEGLULEUARGGLUSERSER
5   ILEPROGLYALAGLYLEUGLYVALTRPALA
6   LYSARGLYSMETGLUALAGLYGLUARGLEU
7   GLYPROCYSVALVALVALPROARGALAALA
8   ALALYSGLUTHRASPPHEGLYTRPGLUGLN
9   ILELEUTHRASPVALGLUVALSERPROGLN
10   GLUGLYCYSILETHRLYSILESERGLUASP
11   LEUGLYSERGLULYSPHECYSVALASPALA
12   ASNGLNALAGLYALAGLYSERTRPLEULYS
13   TYRILEARGVALALACYSSERCYSASPASP
14   GLNASNLEUTHRMETCYSGLNILESERGLU
15   GLNILETYRTYRLYSVALILELYSASPILE
16   GLUPROGLYGLUGLULEULEUVALHISVAL
17   LYSGLUGLYVALTYRPROLEUGLYTHRVAL
18   PROPROGLYLEUASPGLU

Samples:

sample_1: entity, [U-99% 13C; U-99% 15N], 0.45-0.55 mM; potassium phosphate 20 mM; potassium chloride 50 mM; DTT 2.5 mM; H2O 90%; D2O 10%

sample_2: entity, [U-99% 15N], 0.4-0.5 mM; potassium phosphate 20 mM; potassium chloride 50 mM; DTT 2.5 mM; H2O 90%; D2O 10%

sample_3: entity 0.5 mM; potassium phosphate 20 mM; potassium chloride 50 mM; DTT 2.5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.088 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D HBCB(CGCD)HDsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D DQF-COSYsample_3isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1

Software:

VNMRJ, Agilent - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CcpNmr, CCPN - chemical shift assignment, data analysis, peak picking

ARIA, Linge, O'Donoghue and Nilges - refinement, structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

TALOS, Cornilescu, Delaglio and Bax - generation of torsion angle restraints

NMR spectrometers:

  • Varian Varian NMR System 800 MHz
  • Varian Varian NMR System 900 MHz
  • Varian Varian NMR System 500 MHz

Related Database Links:

UNP Q9HAZ2
AlphaFold Q9C0I8

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks