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- PDB-3gfg: Structure of putative oxidoreductase yvaA from Bacillus subtilis ... -

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Basic information

Entry
Database: PDB / ID: 3gfg
TitleStructure of putative oxidoreductase yvaA from Bacillus subtilis in triclinic form
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 / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsRamagopal, U.A. / Toro, R. / Gilmore, M. / Chang, S. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Crystal structure of putative oxidoreductase yvaA from Bacillus subtilis in triclinic form.
Authors: Ramagopal, U.A. / Toro, R. / Gilmore, M. / Chang, S. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / 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 1.4Sep 6, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized oxidoreductase yvaA
B: Uncharacterized oxidoreductase yvaA
C: Uncharacterized oxidoreductase yvaA
D: Uncharacterized oxidoreductase yvaA
E: Uncharacterized oxidoreductase yvaA
F: Uncharacterized oxidoreductase yvaA
G: Uncharacterized oxidoreductase yvaA
H: Uncharacterized oxidoreductase yvaA
I: Uncharacterized oxidoreductase yvaA
J: Uncharacterized oxidoreductase yvaA
K: Uncharacterized oxidoreductase yvaA
L: Uncharacterized oxidoreductase yvaA


Theoretical massNumber of molelcules
Total (without water)495,22312
Polymers495,22312
Non-polymers00
Water9,296516
1
A: Uncharacterized oxidoreductase yvaA
B: Uncharacterized oxidoreductase yvaA


Theoretical massNumber of molelcules
Total (without water)82,5372
Polymers82,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-11.1 kcal/mol
Surface area29720 Å2
MethodPISA
2
C: Uncharacterized oxidoreductase yvaA
D: Uncharacterized oxidoreductase yvaA


Theoretical massNumber of molelcules
Total (without water)82,5372
Polymers82,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-11 kcal/mol
Surface area29040 Å2
MethodPISA
3
E: Uncharacterized oxidoreductase yvaA
F: Uncharacterized oxidoreductase yvaA


Theoretical massNumber of molelcules
Total (without water)82,5372
Polymers82,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-12.9 kcal/mol
Surface area28930 Å2
MethodPISA
4
G: Uncharacterized oxidoreductase yvaA
H: Uncharacterized oxidoreductase yvaA


Theoretical massNumber of molelcules
Total (without water)82,5372
Polymers82,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-10.7 kcal/mol
Surface area28850 Å2
MethodPISA
5
I: Uncharacterized oxidoreductase yvaA
J: Uncharacterized oxidoreductase yvaA


Theoretical massNumber of molelcules
Total (without water)82,5372
Polymers82,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-11.6 kcal/mol
Surface area28660 Å2
MethodPISA
6
K: Uncharacterized oxidoreductase yvaA
L: Uncharacterized oxidoreductase yvaA


Theoretical massNumber of molelcules
Total (without water)82,5372
Polymers82,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-12.8 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.931, 92.135, 187.589
Angle α, β, γ (deg.)95.310, 94.190, 95.210
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized oxidoreductase yvaA


Mass: 41268.543 Da / Num. of mol.: 12 / Fragment: UNP residues 3-358
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


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-tris pH 6.5, 25% PEG 3350, 0.2M NaCl, 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: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 146417 / Num. obs: 146417 / % possible obs: 98.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.074 / Χ2: 1.133 / Net I/σ(I): 11.381
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.77 / Num. unique all: 14589 / Rsym value: 0.307 / Χ2: 0.992 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GDO

3gdo


Resolution: 2.59→45.41 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.841 / SU B: 22.271 / SU ML: 0.218 / SU R Cruickshank DPI: 0.912 / SU Rfree: 0.303 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.912 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 7368 5 %RANDOM
Rwork0.182 ---
obs0.185 146360 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.21 Å2 / Biso mean: 22.11 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.04 Å2-0.87 Å2
2--0.31 Å2-1.04 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.59→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31843 0 0 516 32359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02232550
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.96744097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01954085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14624.3881463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1155713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.47515193
X-RAY DIFFRACTIONr_chiral_restr0.090.24989
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02124427
X-RAY DIFFRACTIONr_mcbond_it0.5681.520251
X-RAY DIFFRACTIONr_mcangle_it1.121232719
X-RAY DIFFRACTIONr_scbond_it1.782312299
X-RAY DIFFRACTIONr_scangle_it3.0724.511364
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 488 -
Rwork0.25 9532 -
all-10020 -
obs--90.52 %
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)
12.41980.33150.22121.21780.07350.93640.01040.0190.382-0.069-0.0098-0.2336-0.13250.0791-0.00060.0430.0210.02940.0907-0.02770.184919.2769.4412.033
22.29290.53450.231.24990.05970.91010.05080.1455-0.1409-0.1529-0.06280.11660.0618-0.04340.0120.05160.0544-0.03390.0948-0.04240.0617-18.472-10.287-3.509
33.14080.30580.17490.93350.01151.0730.08840.14470.5058-0.0727-0.0206-0.2053-0.2010.1034-0.06770.0970.03720.09240.14950.0310.2022-25.1492.23295.372
42.73580.46520.45971.3488-0.01291.05870.11320.3857-0.1487-0.1523-0.0460.1360.1129-0.0629-0.06730.07690.0762-0.02020.1913-0.02520.0411-62.956-17.31689.24
52.304-0.7977-0.32051.49080.41050.7821-0.0529-0.17050.07890.0590.02650.0945-0.0268-0.01350.02630.0097-0.0053-0.00530.0537-0.00520.0377-62.136-14.86138.982
62.3556-0.8893-0.06921.36660.20281.1143-0.0240.0293-0.18070.0390.0724-0.12880.1030.0922-0.04840.01270.004-0.01460.0485-0.02880.1037-24.271-33.572131.148
72.8411-0.64260.10911.18610.00481.1316-0.069-0.40940.05680.08890.04130.1339-0.1478-0.07150.02770.0357-0.0185-0.00540.18910.00050.0611-17.928-3.73546.435
82.5214-0.76630.18221.42020.15821.31190.0641-0.1099-0.38910.07810.0475-0.12020.19980.108-0.11160.03980.0024-0.05270.15280.03610.170719.949-22.93740.353
91.2355-0.06470.63870.9510.23882.0464-0.0128-0.0825-0.10270.22820.0102-0.27750.13040.28520.00260.12180.0196-0.12140.0968-0.00080.3634-7.785-63.387180.075
101.91090.4910.64911.27940.48611.3655-0.14010.23580.0153-0.2040.05480.0724-0.02930.07370.08520.1436-0.0407-0.02460.0505-0.05250.2476-37.005-70.695149.276
111.93070.61571.91251.11620.60912.9325-0.16020.2365-0.1405-0.2110.2404-0.2785-0.01010.3415-0.08020.3285-0.03890.02170.2046-0.18290.3082-47.29839.17789.997
121.87570.27511.07861.72520.88562.2631-0.25150.32740.0274-0.84850.12720.2035-0.24710.12740.12430.8473-0.23-0.12320.2341-0.10910.2649-73.52631.40156.261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 356
2X-RAY DIFFRACTION2B13 - 357
3X-RAY DIFFRACTION3C13 - 357
4X-RAY DIFFRACTION4D13 - 356
5X-RAY DIFFRACTION5E13 - 357
6X-RAY DIFFRACTION6F13 - 357
7X-RAY DIFFRACTION7G13 - 356
8X-RAY DIFFRACTION8H13 - 357
9X-RAY DIFFRACTION9I13 - 357
10X-RAY DIFFRACTION10J13 - 357
11X-RAY DIFFRACTION11K13 - 357
12X-RAY DIFFRACTION12L13 - 357

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