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- PDB-3ec3: Crystal structure of the bb fragment of ERp72 -

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Basic information

Entry
Database: PDB / ID: 3ec3
TitleCrystal structure of the bb fragment of ERp72
ComponentsProtein disulfide-isomerase A4
KeywordsISOMERASE / THIOREDOXIN-LIKE FOLD / Endoplasmic reticulum / Glycoprotein / Redox-active center
Function / homology
Function and homology information


protein-disulfide reductase activity => GO:0015035 / positive regulation of protein folding / protein disulfide-isomerase / endoplasmic reticulum chaperone complex / protein disulfide isomerase activity / smooth endoplasmic reticulum / chaperone-mediated protein folding / response to endoplasmic reticulum stress / cell redox homeostasis / melanosome ...protein-disulfide reductase activity => GO:0015035 / positive regulation of protein folding / protein disulfide-isomerase / endoplasmic reticulum chaperone complex / protein disulfide isomerase activity / smooth endoplasmic reticulum / chaperone-mediated protein folding / response to endoplasmic reticulum stress / cell redox homeostasis / melanosome / protein folding / endoplasmic reticulum lumen / cell surface / endoplasmic reticulum / extracellular space
Similarity search - Function
Protein disulphide-isomerase A4 / Protein disulfide-isomerase A4, TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. ...Protein disulphide-isomerase A4 / Protein disulfide-isomerase A4, TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein disulfide-isomerase A4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: Structure / Year: 2009
Title: Structure of the Noncatalytic Domains and Global Fold of the Protein Disulfide Isomerase ERp72.
Authors: Kozlov, G. / Maattanen, P. / Schrag, J.D. / Hura, G.L. / Gabrielli, L. / Cygler, M. / Thomas, D.Y. / Gehring, K.
History
DepositionAug 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase A4
B: Protein disulfide-isomerase A4


Theoretical massNumber of molelcules
Total (without water)56,6092
Polymers56,6092
Non-polymers00
Water6,990388
1
A: Protein disulfide-isomerase A4


Theoretical massNumber of molelcules
Total (without water)28,3041
Polymers28,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein disulfide-isomerase A4


Theoretical massNumber of molelcules
Total (without water)28,3041
Polymers28,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.171, 62.171, 135.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Protein disulfide-isomerase A4 / Protein ERp-72 / ERp72 / Calcium-binding protein 2 / CaBP2


Mass: 28304.332 Da / Num. of mol.: 2 / Fragment: UNP residues 283-523 / Mutation: E470G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pdia4, Cabp2, Erp70 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P38659, protein disulfide-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLN497 TO ARG CONFLICT IN UNP ENTRY P38659

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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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG MME 2000, 25% glycerol, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9799, 0.9796, 0.9646
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2006
RadiationMonochromator: SI (111) DOUBLE-CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.97961
30.96461
ReflectionResolution: 1.92→50 Å / Num. all: 42416 / Num. obs: 42162 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 20.6
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3075 / % possible all: 95.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.92→19.48 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.417 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.146 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23613 2238 5 %RANDOM
Rwork0.18757 ---
obs0.19011 42162 99.83 %-
all-42233 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.919 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.92→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3689 0 0 388 4077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223773
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9675089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41124.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66715675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6281516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022858
X-RAY DIFFRACTIONr_nbd_refined0.220.21714
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22545
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.224
X-RAY DIFFRACTIONr_mcbond_it1.1411.52351
X-RAY DIFFRACTIONr_mcangle_it1.66423698
X-RAY DIFFRACTIONr_scbond_it2.6131607
X-RAY DIFFRACTIONr_scangle_it3.9684.51391
LS refinement shellResolution: 1.92→1.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 164 -
Rwork0.206 3075 -
obs--99.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.74761.2981-0.99881.57360.19583.68120.2026-0.31630.03670.1109-0.12870.0620.07620.0628-0.07390.074-0.0488-0.01310.0666-0.0060.0444-19.441822.204837.5958
24.20281.74281.74681.8991.10721.3520.01570.3537-0.1893-0.06310.0277-0.03510.03480.0698-0.04340.0577-0.01920.00570.0575-0.01770.0052-14.721320.749629.6015
32.0452-0.4867-1.31281.24570.83373.5982-0.0131-0.0468-0.14390.02510.0425-0.10240.26620.2402-0.02950.0267-0.0079-0.01010.05210.01250.06982.908924.319543.0266
43.73540.0284-1.84443.44790.90936.4571-0.116-0.5938-0.02960.24270.3187-0.420.59411.5733-0.2027-0.11510.1724-0.10330.2892-0.03490.013315.986520.756945.5493
51.0095-0.741-0.4114.7821-0.82533.0769-0.003-0.0048-0.1042-0.23360.09160.1365-0.0207-0.0967-0.08860.1023-0.0281-0.00430.05080.01890.066226.9939-7.593522.1079
60.8356-0.0479-0.24514.7874-1.88731.6805-0.078-0.1092-0.05550.27920.0730.13220.0183-0.04340.00490.0741-0.01730.00480.0266-0.00090.009825.8945-0.478225.6431
71.9043-0.6147-1.3711.57620.73693.69960.04510.05350.0136-0.0311-0.01620.1839-0.1065-0.3606-0.02890.04310.0072-0.01540.02560.00380.066719.612514.673813.0481
84.0232-0.2491-1.36633.78581.08476.48610.33440.49480.381-0.3137-0.09060.1599-1.0687-1.2177-0.24380.05560.2591-0.01270.13030.10610.013910.324124.264110.5446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA282 - 3115 - 34
2X-RAY DIFFRACTION2AA312 - 38835 - 111
3X-RAY DIFFRACTION3AA389 - 452112 - 175
4X-RAY DIFFRACTION4AA453 - 512176 - 235
5X-RAY DIFFRACTION5BB282 - 3255 - 48
6X-RAY DIFFRACTION6BB326 - 38849 - 111
7X-RAY DIFFRACTION7BB389 - 452112 - 175
8X-RAY DIFFRACTION8BB453 - 510176 - 233

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