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- PDB-1xea: Crystal structure of a Gfo/Idh/MocA family oxidoreductase from Vi... -

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Basic information

Entry
Database: PDB / ID: 1xea
TitleCrystal structure of a Gfo/Idh/MocA family oxidoreductase from Vibrio cholerae
ComponentsOxidoreductase, Gfo/Idh/MocA family
KeywordsOXIDOREDUCTASE / Structural Genomics / Protein Structure Initiative / NYSGXRC / T1536 / VCA1048 / Gfo/Idh/MocA family oxidoreductase / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


: / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Oxidoreductase, Gfo/Idh/MocA family
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SAD / Resolution: 2.65 Å
AuthorsR Rajashankar, K. / Reynes, J.A. / Kniewel, R. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a Gfo/Idh/MocA family oxidoreductase from Vibrio cholerae
Authors: R Rajashankar, K. / Reynes, J.A. / Kniewel, R. / Lima, C.D.
History
DepositionSep 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, Gfo/Idh/MocA family
B: Oxidoreductase, Gfo/Idh/MocA family
C: Oxidoreductase, Gfo/Idh/MocA family
D: Oxidoreductase, Gfo/Idh/MocA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8665
Polymers147,8074
Non-polymers591
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-22 kcal/mol
Surface area47170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.529, 112.835, 177.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein
Oxidoreductase, Gfo/Idh/MocA family / Gfo/Idh/MocA family oxidoreductase


Mass: 36951.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VCA1048 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3 / References: UniProt: Q9KKQ4
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.85 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 14% PEG 4000, 0.1M Tris 8.5, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 23, 2004
RadiationMonochromator: Flat Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. all: 90383 / Num. obs: 90383 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.65→2.74 Å / Mean I/σ(I) obs: 1.3 / Num. unique all: 8472 / Rsym value: 0.61 / % possible all: 92.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SAD
Starting model: Experimental electron density map from Se-SAD phasing.

Resolution: 2.65→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 180192.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: A poor molecular replacement solution was obtained using a model derived from pdb entry 1TLT. MR phases were used to locate Selenium sites. One unknown metal ion was located. It was refined ...Details: A poor molecular replacement solution was obtained using a model derived from pdb entry 1TLT. MR phases were used to locate Selenium sites. One unknown metal ion was located. It was refined as partially occupied Ni+2 (may be from purification column).
RfactorNum. reflection% reflectionSelection details
Rfree0.271 4213 4.9 %RANDOM
Rwork0.227 ---
obs0.227 85418 93.2 %-
all-85418 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.2388 Å2 / ksol: 0.348025 e/Å3
Displacement parametersBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1-12.13 Å20 Å20 Å2
2---6.54 Å20 Å2
3----5.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9924 0 1 273 10198
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.433 585 4.7 %
Rwork0.385 11973 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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