BMRB Entry 36001

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36001
MolProbity Validation Chart

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Title:
Structure model of a protein-DNA complex
Deposition date:
2016-06-07
Original release date:
2017-02-20
Authors:
Jin, C.; Hu, Y.; Ding, J.; Zhang, Y.
Citation:

Citation: Guan, Ling; He, Peng; Yang, Fang; Zhang, Yuan; Hu, Yunfei; Ding, Jienv; Hua, Yu; Zhang, Yi; Ye, Qiong; Hu, Jiazhi; Wang, Tao; Jin, Changwen; Kong, Daochun. "Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe"  J. Biol. Chem. 292, 6056-6075 (2017).
PubMed: 28223353

Assembly members:

Assembly members:
entity_1, polymer, 111 residues, 13248.225 Da.
entity_2, polymer, 12 residues, 3638.432 Da.
entity_3, polymer, 12 residues, 3682.424 Da.

Natural source:

Natural source:   Common Name: Fission yeast   Taxonomy ID: 284812   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Schizosaccharomyces Schizosaccharomyces pombe

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AKAQRTHLSLEEKIKLMRLV VRHKHELVDRKTSEFYAKIA RIGYEDEGLAIHTESACRNQ IISIMRVYEQRLAHRQPGMK TTPEEDELDQLCDEWKARLS ELQQYREKFLV
entity_2: CAAAACAATATT
entity_3: AATATTGTTTTG

Data sets:
Data typeCount
13C chemical shifts438
15N chemical shifts98
1H chemical shifts612

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_33

Entities:

Entity 1, entity_1 111 residues - 13248.225 Da.

1   ALALYSALAGLNARGTHRHISLEUSERLEU
2   GLUGLULYSILELYSLEUMETARGLEUVAL
3   VALARGHISLYSHISGLULEUVALASPARG
4   LYSTHRSERGLUPHETYRALALYSILEALA
5   ARGILEGLYTYRGLUASPGLUGLYLEUALA
6   ILEHISTHRGLUSERALACYSARGASNGLN
7   ILEILESERILEMETARGVALTYRGLUGLN
8   ARGLEUALAHISARGGLNPROGLYMETLYS
9   THRTHRPROGLUGLUASPGLULEUASPGLN
10   LEUCYSASPGLUTRPLYSALAARGLEUSER
11   GLULEUGLNGLNTYRARGGLULYSPHELEU
12   VAL

Entity 2, entity_2 12 residues - 3638.432 Da.

1   DCDADADADADCDADADTDA
2   DTDT

Entity 3, entity_3 12 residues - 3682.424 Da.

1   DADADTDADTDTDGDTDTDT
2   DTDG

Samples:

sample_1: Sap1, [U-99% 15N][U-99% 13C; U-99% 15N], 0.5 mM; sodium phosphate 20 mM

sample_2: DNA (5'-CAAAACAATATT-3') 0.7 mM; DNA (5'-GTTTTGTTATAA-3') mM; Sap1, [U-99% 13C; U-99% 15N], 0.5 mM; sodium phosphate 20 mM

sample_3: DNA (5'-CAAAACAATATT-3') 0.5 mM; DNA (5'-GTTTTGTTATAA-3') mM; sodium phosphate 20 mM

sample_conditions_1: ionic strength: 60 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D filtered NOESYsample_2isotropicsample_conditions_1

Software:

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 950 MHz

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