BMRB Entry 11560

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11560
MolProbity Validation Chart

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Title:
Solution structure of the peptidyl prolyl cis-trans isomerase domain of C113D mutant with sulfate ion
Deposition date:
2014-03-25
Original release date:
2014-12-15
Authors:
Xu, Ning; Tamari, Yu; Tochio, Naoya; Tate, Shin-ichi
Citation:

Citation: Xu, Ning; Tochio, Naoya; Wang, Jing; Tamari, Yu; Uewaki, Jun-ichi; Utsunomiya-Tate, Naoko; Igarashi, Kazuhiko; Shiraki, Takuma; Kobayashi, Naohiro; Tate, Shin-ichi. "The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif"  Biochemistry 53, 5568-5578 (2014).
PubMed: 25100325

Assembly members:

Assembly members:
C113D_mutant_hPin1_PPIase_domain, polymer, 117 residues, 13133.786 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: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
C113D_mutant_hPin1_PPIase_domain: GSHMEPARVRCSHLLVKHSQ SRRPSSWRQEKITRTKEEAL ELINGYIQKIKSGEEDFESL ASQFSDDSSAKARGDLGAFS RGQMQKPFEDASFALRTGEM SGPVFTDSGIHIILRTE

Data sets:
Data typeCount
13C chemical shifts504
15N chemical shifts126
1H chemical shifts803

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1C113D mutant human Pin1 PPIase domain1

Entities:

Entity 1, C113D mutant human Pin1 PPIase domain 117 residues - 13133.786 Da.

1   GLYSERHISMETGLUPROALAARGVALARG
2   CYSSERHISLEULEUVALLYSHISSERGLN
3   SERARGARGPROSERSERTRPARGGLNGLU
4   LYSILETHRARGTHRLYSGLUGLUALALEU
5   GLULEUILEASNGLYTYRILEGLNLYSILE
6   LYSSERGLYGLUGLUASPPHEGLUSERLEU
7   ALASERGLNPHESERASPASPSERSERALA
8   LYSALAARGGLYASPLEUGLYALAPHESER
9   ARGGLYGLNMETGLNLYSPROPHEGLUASP
10   ALASERPHEALALEUARGTHRGLYGLUMET
11   SERGLYPROVALPHETHRASPSERGLYILE
12   HISILEILELEUARGTHRGLU

Samples:

sample_1: C113D mutant hPin1 PPIase domain, [U-13C; U-15N], 0.8 mM; sodium sulfate 100 mM; sodium phosphate 50 mM; EDTA 5 mM; DTT 1 mM; sodium azide 0.03%; H2O 94.12%; D2O 5.88%

sample_conditions_1: ionic strength: 100 mM; pH: 6.6; pressure: 1 atm; temperature: 299 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1

Software:

Magro, Kobayashi - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

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

SPARKY, Goddard - data analysis

TOPSPIN, Bruker Biospin - collection

NMRView, Johnson, One Moon Scientific - data analysis

NMR spectrometers:

  • Bruker Avance 700 MHz

Related Database Links:

BMRB 11559
PDB
DBJ BAE02434 BAF83763 BAG11415 BAG53486
EMBL CAG28582
GB AAC50492 AAH02899 AAI12584 AAI58868 AAV38138
PRF 2209428A
REF NP_001029804 NP_001100171 NP_001231300 NP_001270625 NP_006212
SP Q13526 Q4R383 Q5BIN5
TPG DAA28013
AlphaFold Q13526 Q4R383 Q5BIN5

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