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- PDB-2h8l: Crystal structure of the bb' fragment of ERp57 -

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Basic information

Entry
Database: PDB / ID: 2h8l
TitleCrystal structure of the bb' fragment of ERp57
ComponentsProtein disulfide-isomerase A3
KeywordsISOMERASE / thioredoxin-like fold
Function / homology
Function and homology information


Tapasin-ERp57 complex / Calnexin/calreticulin cycle / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / peptide antigen assembly with MHC class I protein complex / phospholipase C activity / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / protein disulfide isomerase activity ...Tapasin-ERp57 complex / Calnexin/calreticulin cycle / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / peptide antigen assembly with MHC class I protein complex / phospholipase C activity / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / protein disulfide isomerase activity / protein-disulfide reductase activity / phagocytic vesicle / extrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / MHC class I peptide loading complex / platelet aggregation / recycling endosome membrane / melanosome / protein folding / ER-Phagosome pathway / adaptive immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / focal adhesion / cell surface / endoplasmic reticulum / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus
Similarity search - Function
Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / 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 A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKozlov, G. / Schrag, J.D. / Cygler, M. / Gehring, K.
CitationJournal: Structure / Year: 2006
Title: Crystal Structure of the bb' Domains of the Protein Disulfide Isomerase ERp57.
Authors: Kozlov, G. / Maattanen, P. / Schrag, J.D. / Pollock, S. / Cygler, M. / Nagar, B. / Thomas, D.Y. / Gehring, K.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase A3
B: Protein disulfide-isomerase A3
C: Protein disulfide-isomerase A3


Theoretical massNumber of molelcules
Total (without water)86,4553
Polymers86,4553
Non-polymers00
Water8,161453
1
A: Protein disulfide-isomerase A3


Theoretical massNumber of molelcules
Total (without water)28,8181
Polymers28,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein disulfide-isomerase A3


Theoretical massNumber of molelcules
Total (without water)28,8181
Polymers28,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein disulfide-isomerase A3


Theoretical massNumber of molelcules
Total (without water)28,8181
Polymers28,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.340, 62.415, 99.293
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6

Dom-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROLEUAA134 - 3656 - 237
2ALATYRBB135 - 3647 - 236
3PROLEUCC134 - 3656 - 237

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Components

#1: Protein Protein disulfide-isomerase A3 / Disulfide isomerase ER-60 / ERp60 / 58 kDa microsomal protein / p58 / ERp57 / 58 kDa glucose-regulated protein


Mass: 28818.490 Da / Num. of mol.: 3 / Fragment: bb' fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA3, ERP60, GRP58 / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30101, protein disulfide-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 3350, 0.1M ammonium sulphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795, 0.9950
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2005
RadiationMonochromator: Si (111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.9951
ReflectionResolution: 2→50 Å / Num. obs: 62742 / % possible obs: 99.4 % / Observed criterion σ(F): 14 / Observed criterion σ(I): 2.6
Reflection shellResolution: 2→2.07 Å / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→32.7 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.012 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.165 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25015 3162 5.1 %RANDOM
Rwork0.19426 ---
obs0.19709 59353 99.64 %-
all-59353 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.14 Å2
2---0.44 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 2→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 0 453 6087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225753
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9437721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7415691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85124.412306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.156151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2481533
X-RAY DIFFRACTIONr_chiral_restr0.1430.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024402
X-RAY DIFFRACTIONr_nbd_refined0.2150.22591
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23864
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2448
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.227
X-RAY DIFFRACTIONr_mcbond_it1.3511.53561
X-RAY DIFFRACTIONr_mcangle_it1.69725517
X-RAY DIFFRACTIONr_scbond_it3.01332505
X-RAY DIFFRACTIONr_scangle_it4.2174.52204
Refine LS restraints NCS

Ens-ID: 1 / Number: 1868 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.75
2Bloose positional0.785
3Cloose positional0.845
1Aloose thermal2.5110
2Bloose thermal2.510
3Cloose thermal2.2810
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 250 -
Rwork0.271 4194 -
obs-4194 96.17 %
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)
14.480.96851.02945.71280.66892.251-0.13530.3610.7974-0.1760.10030.1135-0.41140.04720.035-0.1354-0.0159-0.0183-0.20310.03750.010846.46336.94871.165
21.92810.7922-0.17524.9044-0.02425.2923-0.09490.23260.0821-0.27390.1225-0.07150.2359-0.1883-0.0276-0.1121-0.0755-0.0097-0.183-0.0137-0.195738.1110.10366.688
33.9265-0.02962.02661.4059-0.12094.913-0.1552-0.43770.08420.23090.2219-0.17830.0839-0.45-0.0667-0.02430.02530.031-0.1058-0.0504-0.249536.86-0.68791.24
46.6958-2.52090.30954.22531.34193.3252-0.0537-0.9258-0.40860.36840.31360.938-0.2497-0.8453-0.2599-0.038-0.06870.13430.38760.18890.058610.482-6.78482.094
55.77681.9802-3.8131.82-0.73845.46530.07940.1571-0.4137-0.0957-0.0957-0.17560.10120.04320.0163-0.1678-0.0232-0.0341-0.04530.0064-0.029913.67536.80662.452
66.16761.17692.44242.6848-1.41164.71820.17560.2796-0.7437-0.018-0.03590.02520.28330.4112-0.1397-0.1581-0.01130.0259-0.1312-0.0376-0.0116-7.05224.33478.653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA134 - 2456 - 117
2X-RAY DIFFRACTION2AA246 - 365118 - 237
3X-RAY DIFFRACTION3BB135 - 2457 - 117
4X-RAY DIFFRACTION4BB246 - 364118 - 236
5X-RAY DIFFRACTION5CC134 - 2456 - 117
6X-RAY DIFFRACTION6CC246 - 365118 - 237

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