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- PDB-3hdc: The crystal structure of thioredoxin protein from Geobacter metal... -

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Basic information

Entry
Database: PDB / ID: 3hdc
TitleThe crystal structure of thioredoxin protein from Geobacter metallireducens
ComponentsThioredoxin family protein
KeywordsOXIDOREDUCTASE / thioredoxin / Geobacter metallireducens / GS-15 / ATCC53774 / DSM 7210 / 11211i / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


antioxidant activity / cell redox homeostasis / oxidoreductase activity
Similarity search - Function
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / 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
TlpA family-related protein disulfide reductase
Similarity search - Component
Biological speciesGeobacter metallireducens GS-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.771 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of thioredoxin protein from Geobacter metallireducens
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Derived calculations / Structure summary / Category: struct_conn / struct_keywords
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text
Revision 1.3Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin family protein


Theoretical massNumber of molelcules
Total (without water)17,9991
Polymers17,9991
Non-polymers00
Water3,027168
1
A: Thioredoxin family protein

A: Thioredoxin family protein


Theoretical massNumber of molelcules
Total (without water)35,9982
Polymers35,9982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2740 Å2
ΔGint-10 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.678, 63.678, 94.587
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsdimer, the second molecule is generated by the two fold axis: X-Y, -Y, Z+2/3.

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Components

#1: Protein Thioredoxin family protein


Mass: 17999.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Strain: strain GS-15 / ATCC 53774 / DSM 7210 / Gene: Gmet_1383 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Codon+RIL-Stratagene / References: UniProt: Q39VV7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M Citric acid pH 3.5, 3.0 M Sodium chloride, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 21827 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.378 / Num. unique all: 1063 / % possible all: 100

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Processing

Software
NameClassification
CBASSdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.771→35.9 Å / SU ML: 0.18 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1134 5.2 %RANDOM
Rwork0.1788 ---
obs0.1798 21827 98.59 %-
all-22100 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.239 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 18.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.8818 Å20 Å2-0 Å2
2--2.8818 Å20 Å2
3----5.7636 Å2
Refinement stepCycle: LAST / Resolution: 1.771→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 0 168 1354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7714-1.8520.19661460.16452452X-RAY DIFFRACTION96
1.852-1.94960.20291370.15912500X-RAY DIFFRACTION97
1.9496-2.07170.20711370.16092572X-RAY DIFFRACTION98
2.0717-2.23170.20581330.16492563X-RAY DIFFRACTION99
2.2317-2.45620.18941640.17572565X-RAY DIFFRACTION99
2.4562-2.81150.23971230.19472632X-RAY DIFFRACTION99
2.8115-3.54170.18971350.18312669X-RAY DIFFRACTION100
3.5417-35.90730.17471590.1812740X-RAY DIFFRACTION99

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