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- PDB-4f9z: Crystal Structure of human ERp27 -

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Basic information

Entry
Database: PDB / ID: 4f9z
TitleCrystal Structure of human ERp27
ComponentsEndoplasmic reticulum resident protein 27
KeywordsPEPTIDE BINDING PROTEIN / Thioredoxin fold / ER Foldase / ERp57 / Endoplasmic reticulum
Function / homology
Function and homology information


response to unfolded protein / response to endoplasmic reticulum stress / protein folding / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
Thioredoxin-like domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-PE3 / Endoplasmic reticulum resident protein 27
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKober, F.X. / Koelmel, W. / Kuper, J. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Crystal Structure of the Protein-Disulfide Isomerase Family Member ERp27 Provides Insights into Its Substrate Binding Capabilities.
Authors: Kober, F.X. / Koelmel, W. / Kuper, J. / Drechsler, J. / Mais, C. / Hermanns, H.M. / Schindelin, H.
History
DepositionMay 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Endoplasmic reticulum resident protein 27
A: Endoplasmic reticulum resident protein 27
B: Endoplasmic reticulum resident protein 27
C: Endoplasmic reticulum resident protein 27
E: Endoplasmic reticulum resident protein 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,43120
Polymers126,6745
Non-polymers1,75715
Water11,638646
1
D: Endoplasmic reticulum resident protein 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5715
Polymers25,3351
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endoplasmic reticulum resident protein 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5124
Polymers25,3351
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Endoplasmic reticulum resident protein 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0884
Polymers25,3351
Non-polymers7533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Endoplasmic reticulum resident protein 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8074
Polymers25,3351
Non-polymers4733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endoplasmic reticulum resident protein 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4533
Polymers25,3351
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.832, 68.359, 86.775
Angle α, β, γ (deg.)70.45, 88.16, 64.96
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C
51E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'D' and (resseq 9:207 or resseq 211:227 ) and (not element H)D9 - 207
121chain 'D' and (resseq 9:207 or resseq 211:227 ) and (not element H)D211 - 227
211chain 'A' and (resseq 9:207 or resseq 211:227 ) and (not element H)A9 - 207
221chain 'A' and (resseq 9:207 or resseq 211:227 ) and (not element H)A211 - 227
311chain 'B' and (resseq 9:207 or resseq 211:227 ) and (not element H)B9 - 207
321chain 'B' and (resseq 9:207 or resseq 211:227 ) and (not element H)B211 - 227
411chain 'C' and (resseq 9:207 or resseq 211:227 ) and (not element H)C9 - 207
421chain 'C' and (resseq 9:207 or resseq 211:227 ) and (not element H)C211 - 227
511chain 'E' and (resseq 9:207 or resseq 211:227 ) and (not element H)E9 - 207
521chain 'E' and (resseq 9:207 or resseq 211:227 ) and (not element H)E211 - 227

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Components

#1: Protein
Endoplasmic reticulum resident protein 27 / ER protein 27 / ERp27


Mass: 25334.777 Da / Num. of mol.: 5 / Fragment: Tryptic fragment, UNP residues 29-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C12orf46, ERP27, UNQ781/PRO1575 / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q96DN0
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2946.36
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop8.520% PEG 4000, 150mM sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop8.526% PEG 4000, 125mM sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.110.91841
SYNCHROTRONBESSY 14.12
Detector
TypeIDDetectorDate
RAYONIX MX-2251CCDSep 23, 2011
RAYONIX MX-2252CCDJan 17, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si-111 crystalSINGLE WAVELENGTHMx-ray1
2Si-111 crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→57.81 Å / Num. all: 54973 / Num. obs: 72979 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.178 / Rsym value: 0.113 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.111,295.1
6.32-57.811,297.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→40.675 Å / SU ML: 0.29 / σ(F): 1.97 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 1371 2.5 %RANDOM
Rwork0.1699 ---
all0.1712 54973 --
obs0.171 54932 96.15 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.361 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.0635 Å2-0.3947 Å2-6.5621 Å2
2---4.8668 Å2-0.2829 Å2
3----6.252 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8685 0 92 646 9423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078981
X-RAY DIFFRACTIONf_angle_d1.0712179
X-RAY DIFFRACTIONf_dihedral_angle_d15.6393276
X-RAY DIFFRACTIONf_chiral_restr0.0721410
X-RAY DIFFRACTIONf_plane_restr0.0051568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D1708X-RAY DIFFRACTIONPOSITIONAL0.819
12A1708X-RAY DIFFRACTIONPOSITIONAL0.819
13B1702X-RAY DIFFRACTIONPOSITIONAL0.796
14C1693X-RAY DIFFRACTIONPOSITIONAL0.765
15E1708X-RAY DIFFRACTIONPOSITIONAL0.728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.27860.2931370.24125335533595
2.2786-2.36990.26861400.22765315531395
2.3699-2.47770.27551230.21615311531196
2.4777-2.60830.27551290.20235348534896
2.6083-2.77170.26621550.18985357535796
2.7717-2.98570.24291340.18765355535596
2.9857-3.2860.22651390.175342534296
3.286-3.76120.21031440.15645394539497
3.7612-4.73760.15831350.12655399539997
4.7376-40.68170.17741350.15375405540597

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