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- PDB-5xf7: Crystal structure of human protein disulfide isomerase-like prote... -

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Basic information

Entry
Database: PDB / ID: 5xf7
TitleCrystal structure of human protein disulfide isomerase-like protein of the testis
ComponentsProtein disulfide-isomerase-like protein of the testis
KeywordsCHAPERONE
Function / homology
Function and homology information


protein disulfide isomerase activity / spermatid development / cell migration / cell redox homeostasis / protein folding / multicellular organism development / endoplasmic reticulum
Thioredoxin-like superfamily / Thioredoxin domain / Thioredoxin / Endoplasmic reticulum targeting sequence. / Thioredoxin domain profile. / Thioredoxin-like domain
Protein disulfide-isomerase-like protein of the testis
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.381 Å
AuthorsLi, H. / Li, J. / Liu, Y. / Liang, H.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal and solution structures of human protein-disulfide isomerase-like protein of the testis (PDILT) provide insight into its chaperone activity
Authors: Li, H. / Yang, K. / Wang, W. / Niu, Y. / Li, J. / Dong, Y. / Liu, Y. / Wang, C.C. / Wang, L. / Liang, H.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein disulfide-isomerase-like protein of the testis


Theoretical massNumber of molelcules
Total (without water)66,3441
Polymers66,3441
Non-polymers00
Water1,44180
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23520 Å2
Unit cell
γ
α
β
Length a, b, c (Å)97.361, 97.361, 57.588
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein/peptide Protein disulfide-isomerase-like protein of the testis


Mass: 66344.344 Da / Num. of mol.: 1 / Fragment: UNP residues 21-584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDILT / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N807
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 21% (w/v) PEG 3350 and 0.1 M succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 24401 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rsym value: 0.066 / Net I/σ(I): 20.6
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.716 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
PHENIX(1.10_2155: ???)model building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EKZ, 4NWY
Resolution: 2.381→28.106 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 1996 8.18 %
Rwork0.1971 --
Obs0.2003 24401 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.381→28.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 0 80 3844
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0083843
f_angle_d0.9575179
f_dihedral_angle_d14.6772323
f_chiral_restr0.055581
f_plane_restr0.005657
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3805-2.440.34471360.2893160799
2.44-2.50590.36861440.28131618100
2.5059-2.57960.33221400.27511582100
2.5796-2.66280.3311420.25971582100
2.6628-2.75790.25151420.24521647100
2.7579-2.86820.29671460.24021601100
2.8682-2.99860.31561360.24331587100
2.9986-3.15650.27351390.2321590100
3.1565-3.3540.25551470.23841635100
3.354-3.61250.26791380.20511611100
3.6125-3.97510.21041440.19491583100
3.9751-4.54820.1991450.16521605100
4.5482-5.72230.21321550.1599155799
5.7223-28.10760.16931420.1496160099

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