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- PDB-3gyk: The crystal structure of a thioredoxin-like oxidoreductase from S... -

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Basic information

Entry
Database: PDB / ID: 3gyk
TitleThe crystal structure of a thioredoxin-like oxidoreductase from Silicibacter pomeroyi DSS-3
Components27kDa outer membrane protein
KeywordsOXIDOREDUCTASE / APC61738.2 / Silicibacter pomeroyi DSS-3 / thioredoxin-like / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
27kDa outer membrane protein
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsFan, Y. / Marshall, N. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a thioredoxin-like oxidoreductase from Silicibacter pomeroyi DSS-3
Authors: Fan, Y. / Marshall, N. / Keigher, L. / Joachimiak, A.
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
A: 27kDa outer membrane protein
B: 27kDa outer membrane protein
C: 27kDa outer membrane protein
D: 27kDa outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,34125
Polymers77,5274
Non-polymers1,81321
Water13,547752
1
A: 27kDa outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7325
Polymers19,3821
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 27kDa outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7325
Polymers19,3821
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 27kDa outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8907
Polymers19,3821
Non-polymers5086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 27kDa outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9868
Polymers19,3821
Non-polymers6047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.836, 91.700, 67.911
Angle α, β, γ (deg.)90.00, 120.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN. IT IS PREDICTED TO BE MONOMERIC.

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Components

#1: Protein
27kDa outer membrane protein


Mass: 19381.854 Da / Num. of mol.: 4 / Fragment: UNP residues 71-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Strain: DSS-3 / Gene: SPOA0362 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q5LKL9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Lithium sulfate, 0.1M Tris-HCl, 2.0M Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97953 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 25, 2009 / Details: mirror
RadiationMonochromator: Si(111) crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 71433 / Num. obs: 71433 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 35
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3518 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
ARP/wARPmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.076 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.11
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19753 3606 5.1 %RANDOM
Rwork0.16006 ---
all0.16194 67725 --
obs0.16194 67725 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.254 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 99 752 6174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225979
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9628189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3255790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64824.322317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54715939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0651557
X-RAY DIFFRACTIONr_chiral_restr0.1010.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214833
X-RAY DIFFRACTIONr_mcbond_it0.6711.53722
X-RAY DIFFRACTIONr_mcangle_it1.16425998
X-RAY DIFFRACTIONr_scbond_it2.25532257
X-RAY DIFFRACTIONr_scangle_it3.3484.52179
LS refinement shellResolution: 1.76→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 232 -
Rwork0.218 4881 -
obs--99.82 %
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)
12.57390.6541-0.21462.3784-0.68981.7748-0.00460.0381-0.0867-0.1193-0.0061-0.11130.2221-0.01320.01080.07450.0078-0.0310.0027-0.00680.03116.91228.41625.427
21.70380.26570.31182.423-0.92932.63850.0576-0.02060.18050.16640.00410.0855-0.1427-0.0452-0.06160.02110.0043-0.00350.0029-0.01060.0749-8.64334.75352.212
32.1350.76750.27825.1990.04131.4738-0.0151-0.04730.12430.0576-0.10590.3785-0.0387-0.06470.1210.02070.0146-0.02370.0166-0.02670.084225.87812.39340.807
41.6579-0.30320.48925.059-0.66231.66170.11440.0955-0.1287-0.3687-0.09830.13210.07660.0014-0.01610.06290.0171-0.04570.0198-0.02490.050314.21750.47560.616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 171
2X-RAY DIFFRACTION2B0 - 171
3X-RAY DIFFRACTION3C-1 - 170
4X-RAY DIFFRACTION4D0 - 171

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