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- PDB-3gdo: Crystal structure of putative oxidoreductase yvaA from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 3gdo
TitleCrystal structure of putative oxidoreductase yvaA from Bacillus subtilis
ComponentsUncharacterized oxidoreductase yvaA
KeywordsOXIDOREDUCTASE / structural genomics / Putative oxidoreductase yvaA / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


scyllo-inositol 2-dehydrogenase (NADP+) / scyllo-inositol dehydrogenase (NADP+) activity / NADP+ binding / NADPH binding
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / 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 ...Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / 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
scyllo-inositol 2-dehydrogenase (NADP(+)) IolW
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of putative oxidoreductase yvaA from Bacillus subtilis.
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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 1.3Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: 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
A: Uncharacterized oxidoreductase yvaA
B: Uncharacterized oxidoreductase yvaA


Theoretical massNumber of molelcules
Total (without water)80,4242
Polymers80,4242
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-12.6 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.324, 151.309, 56.395
Angle α, β, γ (deg.)90.000, 107.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized oxidoreductase yvaA


Mass: 40212.203 Da / Num. of mol.: 2 / Fragment: UNP residues 12-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU33530, yvaA / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32223
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Tris-HCl pH 8.5, 25% PEG 3350, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2008
RadiationMonochromator: Si(111) Double crystal / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 49833 / Num. obs: 49833 / % possible obs: 98.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.087 / Rsym value: 0.078 / Χ2: 1.311 / Net I/σ(I): 22.131
Reflection shellResolution: 2.03→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4348 / Rsym value: 0.362 / Χ2: 0.862 / % possible all: 86.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.81 / SU B: 4.835 / SU ML: 0.132 / SU R Cruickshank DPI: 0.197 / SU Rfree: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2533 5.1 %RANDOM
Rwork0.204 ---
obs0.206 49797 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.11 Å2 / Biso mean: 40.285 Å2 / Biso min: 20.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å2-2.02 Å2
2---1.03 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 0 0 124 5409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225448
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9697387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25924.435248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01115965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.281533
X-RAY DIFFRACTIONr_chiral_restr0.1060.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214099
X-RAY DIFFRACTIONr_mcbond_it0.9091.53380
X-RAY DIFFRACTIONr_mcangle_it1.6325469
X-RAY DIFFRACTIONr_scbond_it2.49932068
X-RAY DIFFRACTIONr_scangle_it4.034.51911
LS refinement shellResolution: 2.03→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 164 -
Rwork0.281 3016 -
all-3180 -
obs--85.23 %

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