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- PDB-4wbx: Conserved hypothetical protein PF1771 from Pyrococcus furiosus so... -

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Basic information

Entry
Database: PDB / ID: 4wbx
TitleConserved hypothetical protein PF1771 from Pyrococcus furiosus solved by sulfur SAD using Swiss Light Source data
Components2-keto acid:ferredoxin oxidoreductase subunit alpha
KeywordsOXIDOREDUCTASE / Sulfur SAD / case studies / Swiss Light Source / Southeast Collaboratory for Structural genomics / SECSG
Function / homology
Function and homology information


organic acid metabolic process / sulfur compound biosynthetic process / organic substance biosynthetic process / oxidoreductase activity
Similarity search - Function
Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain / Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-keto acid:ferredoxin oxidoreductase subunit alpha
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsWeinert, T. / Waltersperger, S. / Olieric, V. / Panepucci, E. / Chen, L. / Rose, J.P. / Wang, M. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination.
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionSep 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Other
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 24, 2018Group: Other / Structure summary
Category: audit_author / pdbx_database_status / struct_keywords
Item: _audit_author.name / _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 2-keto acid:ferredoxin oxidoreductase subunit alpha


Theoretical massNumber of molelcules
Total (without water)44,0961
Polymers44,0961
Non-polymers00
Water30617
1
C: 2-keto acid:ferredoxin oxidoreductase subunit alpha

C: 2-keto acid:ferredoxin oxidoreductase subunit alpha

C: 2-keto acid:ferredoxin oxidoreductase subunit alpha

C: 2-keto acid:ferredoxin oxidoreductase subunit alpha


Theoretical massNumber of molelcules
Total (without water)176,3864
Polymers176,3864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y+1/2,-z-1/21
crystal symmetry operation11_454-x-1/2,y,-z-1/21
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area9530 Å2
ΔGint-60 kcal/mol
Surface area40570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.020, 126.820, 155.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein 2-keto acid:ferredoxin oxidoreductase subunit alpha


Mass: 44096.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1771 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U046
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.07 M SODIUM ACETATE BUFFER CONTAINING 0.14 M CACL2 14% (V/V) ISOPROPANOL AND 30% (V/V) GLYCEROL
PH range: 6.54.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.066 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 2.301→50 Å / Num. all: 20104 / Num. obs: 18037 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 62.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
BUSTERrefinement
Cootmodel building
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.301→19.627 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 36.17 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 3445 9.97 %PHENIX
Rwork0.2334 ---
obs0.2378 34550 89.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→19.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 0 19 2258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012284
X-RAY DIFFRACTIONf_angle_d1.2653101
X-RAY DIFFRACTIONf_dihedral_angle_d15.496811
X-RAY DIFFRACTIONf_chiral_restr0.047355
X-RAY DIFFRACTIONf_plane_restr0.007402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3013-2.33280.51210.5177231X-RAY DIFFRACTION16
2.3328-2.3660.5261650.4899574X-RAY DIFFRACTION41
2.366-2.40130.4977860.4796794X-RAY DIFFRACTION59
2.4013-2.43880.43451090.451981X-RAY DIFFRACTION70
2.4388-2.47870.42511200.44051069X-RAY DIFFRACTION78
2.4787-2.52130.46571410.38631257X-RAY DIFFRACTION90
2.5213-2.56710.38831500.33191368X-RAY DIFFRACTION99
2.5671-2.61630.34031490.30751362X-RAY DIFFRACTION99
2.6163-2.66960.38211540.29421399X-RAY DIFFRACTION100
2.6696-2.72750.29241520.28061371X-RAY DIFFRACTION100
2.7275-2.79080.33841490.27141373X-RAY DIFFRACTION100
2.7908-2.86040.3441550.28331395X-RAY DIFFRACTION100
2.8604-2.93750.34741520.25091388X-RAY DIFFRACTION100
2.9375-3.02360.36291530.25751381X-RAY DIFFRACTION100
3.0236-3.12080.30041540.25421387X-RAY DIFFRACTION99
3.1208-3.23190.32351510.25751372X-RAY DIFFRACTION99
3.2319-3.36070.3311510.26541359X-RAY DIFFRACTION99
3.3607-3.51280.31951570.25031371X-RAY DIFFRACTION99
3.5128-3.69690.26781520.23511370X-RAY DIFFRACTION99
3.6969-3.92670.25341530.22491372X-RAY DIFFRACTION99
3.9267-4.22710.27031530.19691384X-RAY DIFFRACTION100
4.2271-4.64740.23721520.18161382X-RAY DIFFRACTION100
4.6474-5.30820.19171580.17241390X-RAY DIFFRACTION100
5.3082-6.64450.25471550.2251375X-RAY DIFFRACTION100
6.6445-19.62820.21291530.19151400X-RAY DIFFRACTION100

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