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- PDB-1yd7: Conserved hypothetical protein Pfu-1647980-001 from Pyrococcus fu... -

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Basic information

Entry
Database: PDB / ID: 1yd7
TitleConserved hypothetical protein Pfu-1647980-001 from Pyrococcus furiosus
Components2-keto acid:ferredoxin oxidoreductase subunit alpha
KeywordsOXIDOREDUCTASE / Structural Genomics / Southeast Collaboratory for Structural Genomics / SECSG / Protein Structure Initiative / PSI / conserved hypothetical protein / Pyrococcus furiosus / hyperthermophile
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 / SAS / sad / Resolution: 2.3 Å
AuthorsHoranyi, P. / Florence, Q. / Zhou, W. / Chang, J. / Zhao, M. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. ...Horanyi, P. / Florence, Q. / Zhou, W. / Chang, J. / Zhao, M. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Tempel, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Conserved hypothetical protein Pfu-1647980-001 from Pyrococcus furiosus
Authors: Horanyi, P. / Florence, Q. / Zhou, W. / Chang, J. / Zhao, M. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Tempel, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney ...Authors: Horanyi, P. / Florence, Q. / Zhou, W. / Chang, J. / Zhao, M. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Tempel, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / 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 / _pdbx_database_related.db_name / _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
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,6597
Polymers44,6591
Non-polymers06
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.448, 61.448, 129.084
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

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


Mass: 44659.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U046
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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

Crystal growTemperature: 291 K / Method: modified microbatch / pH: 8.9
Details: 0.1M TRIS-HCl/NaOH, 0.5M ammonium sulfate, pH 8.9, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 17709 / Rmerge(I) obs: 0.08
Reflection shell
Resolution (Å)Rmerge(I) obs% possible all
1.9-1.970.47719.4
1.97-2.050.5234.5
2.05-2.140.44256.5
2.14-2.250.35982.6
2.25-2.390.31597
2.39-2.580.23799.9
2.58-2.840.15399.8
2.84-3.250.096100
3.25-4.090.065100
4.09-300.058100

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Phasing

PhasingMethod: sad
Phasing MADD res high: 2.6 Å / D res low: 20 Å / FOM : 0.39 / Reflection: 8669
Phasing MAD shell
Resolution (Å)FOM Reflection
8.81-200.43477
5.75-8.810.48733
4.55-5.750.46942
3.88-4.550.471082
3.44-3.880.431222
3.12-3.440.391323
2.88-3.120.311417
2.68-2.880.261473
Phasing dmFOM : 0.62 / FOM acentric: 0.61 / FOM centric: 0.66 / Reflection: 11169 / Reflection acentric: 10141 / Reflection centric: 1028
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.9-19.9460.930.930.81496387109
4.3-6.90.890.90.7715191321198
3.4-4.30.860.870.8118601683177
3-3.40.720.720.6619021732170
2.6-30.50.490.6533253090235
2.4-2.60.220.220.2420671928139

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
RefinementMethod to determine structure: SAS / Resolution: 2.3→29.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.577 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24274 630 5 %RANDOM
Rwork0.20586 ---
obs0.20764 12041 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.163 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 6 25 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221305
X-RAY DIFFRACTIONr_bond_other_d0.0010.021223
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9671778
X-RAY DIFFRACTIONr_angle_other_deg0.88932824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13624.15153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34415202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.657157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
X-RAY DIFFRACTIONr_nbd_refined0.20.2245
X-RAY DIFFRACTIONr_nbd_other0.180.21188
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2642
X-RAY DIFFRACTIONr_nbtor_other0.0830.2758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0432919
X-RAY DIFFRACTIONr_mcbond_other0.7082338
X-RAY DIFFRACTIONr_mcangle_it4.05931370
X-RAY DIFFRACTIONr_scbond_it2.4822497
X-RAY DIFFRACTIONr_scangle_it3.5593408
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 47 -
Rwork0.257 873 -
obs--98.71 %

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