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- PDB-3uvt: Crystal structure of the third catalytic domain of ERp46 -

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Basic information

Entry
Database: PDB / ID: 3uvt
TitleCrystal structure of the third catalytic domain of ERp46
ComponentsThioredoxin domain-containing protein 5
KeywordsISOMERASE / thioredoxin-like fold
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / protein disulfide-isomerase / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity / protein-disulfide reductase activity / lysosomal lumen / azurophil granule lumen / protein folding / endoplasmic reticulum lumen ...Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / protein disulfide-isomerase / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity / protein-disulfide reductase activity / lysosomal lumen / azurophil granule lumen / protein folding / endoplasmic reticulum lumen / Neutrophil degranulation / negative regulation of apoptotic process / endoplasmic reticulum / extracellular exosome / extracellular region
Similarity search - Function
: / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...: / 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
Thioredoxin domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKozlov, G. / Gulerez, I.E. / Gehring, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the third catalytic domain of the protein disulfide isomerase ERp46.
Authors: Gulerez, I.E. / Kozlov, G. / Rosenauer, A. / Gehring, K.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin domain-containing protein 5
B: Thioredoxin domain-containing protein 5
C: Thioredoxin domain-containing protein 5
D: Thioredoxin domain-containing protein 5
E: Thioredoxin domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,45010
Polymers60,9695
Non-polymers4805
Water6,593366
1
A: Thioredoxin domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2902
Polymers12,1941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2902
Polymers12,1941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thioredoxin domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2902
Polymers12,1941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thioredoxin domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3863
Polymers12,1941
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Thioredoxin domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)12,1941
Polymers12,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.106, 61.886, 71.002
Angle α, β, γ (deg.)90.00, 106.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thioredoxin domain-containing protein 5 / Endoplasmic reticulum resident protein 46 / ER protein 46 / ERp46 / Thioredoxin-like protein p46


Mass: 12193.891 Da / Num. of mol.: 5 / Fragment: catalytic domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXNDC5, TLP46, UNQ364/PRO700 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NBS9, protein disulfide-isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 3, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2→68.12 Å / Num. all: 36285 / Num. obs: 36285 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 21
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F8U

3f8u


Resolution: 2→68.12 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.43 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.205 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24549 1912 5 %RANDOM
Rwork0.20391 ---
all0.207 36285 --
obs0.20599 36285 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20.21 Å2
2---0.33 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 2→68.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 25 366 4438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224206
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9645693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9895529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13823.064173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6715708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5161527
X-RAY DIFFRACTIONr_chiral_restr0.0720.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023119
X-RAY DIFFRACTIONr_nbd_refined0.1750.21756
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22785
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.239
X-RAY DIFFRACTIONr_mcbond_it0.441.52693
X-RAY DIFFRACTIONr_mcangle_it0.77224183
X-RAY DIFFRACTIONr_scbond_it1.04331723
X-RAY DIFFRACTIONr_scangle_it1.7194.51504
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 142 -
Rwork0.221 2461 -
obs--93.13 %
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)
12.79250.66690.90543.0852-0.44910.69880.03440.0363-0.1440.06810.08220.0285-0.0116-0.0068-0.11660.0023-0.00340.0190.0133-0.00770.06150.9593-9.6005-3.5614
23.01491.25450.32282.50370.04561.4538-0.02120.2621-0.19420.00160.1138-0.08910.0361-0.0218-0.0926-0.002-0.002-0.00320.0242-0.02460.05234.5966-8.8732-8.3861
34.23054.2334-2.65147.6595-1.99053.053-0.29470.1139-0.4956-0.9180.1722-0.44570.51830.17230.12250.07610.03330.0281-0.0171-0.08980.07175.5319-20.0876-9.7062
42.8459-0.2943-0.40360.2946-0.45671.7080.03520.01750.08770.0395-0.0426-0.0753-0.0802-0.02650.00740.0235-0.01470.00390.01550.00480.0714-23.6753-20.57674.4039
53.0325-0.1171-1.06421.2713-0.37171.6571-0.0570.1265-0.11180.01460.0642-0.0254-0.0594-0.1228-0.00710.0121-0.0025-0.00120.02560.00360.0419-27.9759-23.82432.3091
67.54552.05650.98262.6394-0.0612.0069-0.14990.32960.0653-0.12690.0155-0.1597-0.1637-0.09090.13440.04540.0070.03290.06870.0148-0.0372-27.8901-19.3061-9.3918
73.17251.76172.2322.54932.88243.28850.3383-0.385-0.13360.5218-0.3215-0.21350.6902-0.4112-0.01680.1524-0.1461-0.0150.07150.0874-0.016-29.9383-3.902224.0058
81.4885-0.4552-0.04234.12772.58634.13240.2201-0.27-0.02160.3827-0.0738-0.50780.21120.0218-0.14630.017-0.072-0.03790.04330.0561-0.0208-25.042.390920.9313
90.07750.14530.4842.05610.45073.14160.0503-0.0657-0.07890.00710.0074-0.1626-0.0174-0.2564-0.05770.0257-0.04510.01590.0651-0.00780.0126-31.39943.531913.6536
102.24420.050.62060.5196-0.44251.6062-0.04320.0969-0.2598-0.0213-0.01270.0041-0.08330.01680.0560.02160.00180.01430.0678-0.01720.019-21.22710.8777-20.3007
1113.5903-3.4885-4.91665.4375-0.140110.1749-0.19450.5048-0.3513-0.5872-0.04430.36740.6875-0.37360.23870.1288-0.07870.00970.0743-0.0929-0.0505-19.5191-0.2985-33.855
121.16680.32070.35891.4095-0.77081.9775-0.0958-0.0362-0.1355-0.02030.0191-0.04-0.27370.01860.07670.0567-0.00980.00980.0632-0.0163-0.0149-17.75327.2855-20.6836
135.01171.1581-1.38655.0259-0.81042.6006-0.54240.40480.596-0.10690.53460.3413-0.2933-0.01690.00780.16960.0099-0.153-0.01770.04640.06710.74870.479519.5041
1433.41531.95338.35094.5304-3.32837.8180.2287-1.80980.310.558-0.18080.7676-0.869-0.8417-0.0479-0.00170.2922-0.0126-0.0297-0.270.20374.0516-4.173332.735
1524.23822.282820.62850.71370.487321.805-0.8891-0.27491.38940.06380.17721.1056-1.7596-0.02060.71190.16040.1367-0.1873-0.1261-0.12960.173110.9323-1.190627.1566
1662.63820.4058-2.794212.1352-1.928610.4106-1.4248-2.26352.8075-2.62422.17041.6007-1.9318-2.4398-0.74560.4675-0.0974-0.57010.33210.37680.00084.9125-5.430811.7376
175.56582.6497-1.48218.855-1.66112.7045-0.70570.37240.2586-1.0520.50040.4106-0.1092-0.15530.20530.33880.0249-0.1905-0.04710.0332-0.094511.1871-9.346719.2716
187.46621.6374-3.67313.56391.07526.9142-0.2425-0.53080.25180.0018-0.09640.1291-0.8317-0.33830.3390.18140.2152-0.06040.0718-0.0153-0.09969.5386-12.979931.4353
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A322 - 365
2X-RAY DIFFRACTION2A366 - 404
3X-RAY DIFFRACTION3A405 - 428
4X-RAY DIFFRACTION4B321 - 362
5X-RAY DIFFRACTION5B363 - 407
6X-RAY DIFFRACTION6B408 - 428
7X-RAY DIFFRACTION7C319 - 345
8X-RAY DIFFRACTION8C346 - 388
9X-RAY DIFFRACTION9C389 - 428
10X-RAY DIFFRACTION10D322 - 360
11X-RAY DIFFRACTION11D361 - 371
12X-RAY DIFFRACTION12D372 - 428
13X-RAY DIFFRACTION13E324 - 346
14X-RAY DIFFRACTION14E353 - 370
15X-RAY DIFFRACTION15E371 - 379
16X-RAY DIFFRACTION16E383 - 392
17X-RAY DIFFRACTION17E393 - 410
18X-RAY DIFFRACTION18E411 - 428

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