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- PDB-3oqb: CRYSTAL STRUCTURE OF putative oxidoreductase from Bradyrhizobium ... -

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Basic information

Entry
Database: PDB / ID: 3oqb
TitleCRYSTAL STRUCTURE OF putative oxidoreductase from Bradyrhizobium japonicum USDA 110
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


NADPH regeneration / oxidoreductase activity / cytoplasm
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
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / 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 from Bradyrhizobium japonicum USDA 110
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
C: Oxidoreductase
D: Oxidoreductase
E: Oxidoreductase
F: Oxidoreductase
G: Oxidoreductase
H: Oxidoreductase


Theoretical massNumber of molelcules
Total (without water)349,2588
Polymers349,2588
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35260 Å2
ΔGint-150 kcal/mol
Surface area114950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.705, 163.853, 117.726
Angle α, β, γ (deg.)90.000, 103.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxidoreductase /


Mass: 43657.258 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: BAC48105.1, blr2840 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q89RD2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M K/Na tartrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 209402 / % possible obs: 99.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.108 / Χ2: 1.443 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.642.70.861104270.94399.8
2.64-2.692.70.736105670.97899.9
2.69-2.742.70.621104570.96599.8
2.74-2.82.70.57104320.98499.8
2.8-2.862.70.489104580.97799.7
2.86-2.932.70.406106071.01199.8
2.93-32.70.344103531.06399.7
3-3.082.70.271104571.06999.7
3.08-3.172.70.239104361.06499.8
3.17-3.282.70.196105221.12899.8
3.28-3.392.70.163104191.21799.7
3.39-3.532.70.133104021.37999.7
3.53-3.692.80.108105371.49199.8
3.69-3.882.80.094104951.75999.8
3.88-4.132.80.082104871.99599.8
4.13-4.452.80.072104522.19199.8
4.45-4.892.80.061105012.01499.6
4.89-5.62.80.058104391.90399.8
5.6-7.052.90.059104871.965100
7.05-502.90.038104672.39799.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.99 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2276 / WRfactor Rwork: 0.1768 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8432 / SU B: 25.713 / SU ML: 0.248 / SU R Cruickshank DPI: 1.4115 / SU Rfree: 0.3216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 5257 5 %RANDOM
Rwork0.1932 ---
obs0.1959 105429 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 146.67 Å2 / Biso mean: 55.7566 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.1 Å2
2--0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23982 0 0 265 24247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02224542
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.93333219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23453001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29123.6391220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.719154102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39815196
X-RAY DIFFRACTIONr_chiral_restr0.0860.23528
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118936
X-RAY DIFFRACTIONr_mcbond_it0.8123.514901
X-RAY DIFFRACTIONr_mcangle_it3.625023867
X-RAY DIFFRACTIONr_scbond_it8.317509641
X-RAY DIFFRACTIONr_scangle_it0.714.59352
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 373 -
Rwork0.28 7249 -
all-7622 -
obs--99.67 %
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)
10.6141-0.07310.27250.916-0.32340.7570.12470.0284-0.0997-0.1230.06790.18310.27640.0191-0.19260.17490.0226-0.05190.01730.02590.127-35.471519.934833.7934
20.68750.06970.19820.81890.14320.5747-0.0942-0.11460.27750.08390.0524-0.0612-0.02060.00390.04180.02750.0326-0.03190.0515-0.01370.188316.82981.651822.1294
30.627-0.1190.09060.3970.02930.79890.01240.00270.09960.0656-0.01470.0075-0.02840.17010.00240.07670.03570.00170.0795-0.00570.019511.011448.828659.4068
40.636-0.0504-0.03330.60310.1070.66720.0137-0.0580.17140.0580.0480.0231-0.1260.0312-0.06180.06570.00770.02270.01390.00090.1545-32.715786.772220.9817
50.301-0.02330.19520.7080.31161.16320.01210.1079-0.0124-0.05220.02790.07020.1158-0.0068-0.040.0338-0.0157-0.03210.06980.02810.0554-40.131253.8654-2.426
60.505-0.02690.00040.77850.27390.7664-0.01760.0913-0.06670.00180.02720.02540.20110.1834-0.00960.15270.12980.00050.1354-0.01030.013314.158621.840528.5623
70.5623-0.02030.04540.7436-0.00391.3475-0.0828-0.1910.10410.21650.07860.1652-0.2069-0.0250.00410.1570.0940.08190.10760.02010.1006-38.647153.71757.8033
80.78530.0545-0.13070.5925-0.07760.9518-0.08040.2476-0.0159-0.0786-0.0109-0.04330.2434-0.00670.09130.0808-0.00570.03990.11840.0010.02988.547454.1902-7.9486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999

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