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- PDB-3on3: The crystal structure of keto/oxoacid ferredoxin oxidoreductase, ... -

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Basic information

Entry
Database: PDB / ID: 3on3
TitleThe crystal structure of keto/oxoacid ferredoxin oxidoreductase, gamma subunit from Geobacter sulfurreducens PCA
ComponentsKeto/oxoacid ferredoxin oxidoreductase, gamma subunit
KeywordsOXIDOREDUCTASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors
Similarity search - Function
: / Pyruvate-ferredoxin Oxidoreductase; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-oxoglutarate:ferredoxin oxidoreductase, gamma subunit
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.193 Å
AuthorsTan, K. / Zhang, R. / Hatzos, C. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of keto/oxoacid ferredoxin oxidoreductase, gamma subunit from Geobacter sulfurreducens PCA
Authors: Tan, K. / Zhang, R. / Hatzos, C. / Buck, K. / Joachimiak, A.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 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_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_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: Keto/oxoacid ferredoxin oxidoreductase, gamma subunit
B: Keto/oxoacid ferredoxin oxidoreductase, gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7374
Polymers38,5452
Non-polymers1922
Water82946
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-46 kcal/mol
Surface area14320 Å2
MethodPISA
2
A: Keto/oxoacid ferredoxin oxidoreductase, gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3682
Polymers19,2721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Keto/oxoacid ferredoxin oxidoreductase, gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3682
Polymers19,2721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.332, 91.332, 74.191
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsExperimentally unknown. It is predicted that the chains A and B are monomeric.

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Components

#1: Protein Keto/oxoacid ferredoxin oxidoreductase, gamma subunit


Mass: 19272.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU1470 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q74D49
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium chloride, 0.1M Sodium cacodylate, 2M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.193→40 Å / Num. all: 18254 / Num. obs: 18254 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 20.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.5 / Num. unique all: 796 / % possible all: 85.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.193→39.548 Å / SU ML: 0.32 / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 874 5.17 %random
Rwork0.1955 ---
all0.1988 16900 --
obs0.1988 16900 90.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.117 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.6105 Å2-0 Å20 Å2
2---10.6105 Å2-0 Å2
3---21.221 Å2
Refinement stepCycle: LAST / Resolution: 2.193→39.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 10 46 2553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072533
X-RAY DIFFRACTIONf_angle_d1.0223423
X-RAY DIFFRACTIONf_dihedral_angle_d17.544901
X-RAY DIFFRACTIONf_chiral_restr0.068404
X-RAY DIFFRACTIONf_plane_restr0.003447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1935-2.33090.32821340.23372138X-RAY DIFFRACTION74
2.3309-2.51090.26541370.21822507X-RAY DIFFRACTION86
2.5109-2.76350.2421480.20222662X-RAY DIFFRACTION91
2.7635-3.16320.27981570.19392773X-RAY DIFFRACTION94
3.1632-3.98470.24741470.17072873X-RAY DIFFRACTION97
3.9847-39.55430.25361510.19893073X-RAY DIFFRACTION99
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)
12.7635-0.57691.43662.49850.4761.18720.3421-1.0415-0.42630.11350.08450.32860.1312-0.8144-0.30070.2045-0.0355-0.06090.67410.19460.52568.809930.62819.6312
24.28610.257-0.00342.9226-0.36961.2698-0.03-0.04240.4942-0.14450.02270.1283-0.1247-0.13920.03380.23190.04170.00180.20790.00930.203134.132741.266814.8474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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