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- PDB-9nz6: Oxidoreductase isolated from Xanthomonas citri pv. citri A306 -

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Basic information

Entry
Database: PDB / ID: 9nz6
TitleOxidoreductase isolated from Xanthomonas citri pv. citri A306
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / Reductase / flavin / NADH / NADPH
Function / homologymethylglyoxal catabolic process / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / oxidoreductase activity / Oxidoreductase
Function and homology information
Biological speciesXanthomonas citri pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsSantos, L.S. / Torres, S.C. / Balan, A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2023/15874-8 Brazil
CitationJournal: To Be Published
Title: Oxidoreductase isolated from Xanthomonas citri pv. citri A306
Authors: Santos, L.S. / Torres, S.C. / Balan, A.
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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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)322,3948
Polymers322,3948
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21070 Å2
ΔGint-66 kcal/mol
Surface area88180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.620, 129.756, 228.937
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein
Oxidoreductase


Mass: 40299.223 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri pv. citri (bacteria) / Strain: 306 / Gene: XAC3199 / Plasmid: pET28a / Details (production host): 6xHis + Thrombin at N-term / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAI7ZHB9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 17% PEG 6000, 0.2 M NaCl, 0.05 M MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.978→112.885 Å / Num. obs: 55278 / % possible obs: 94.7 % / Redundancy: 13.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.54 / Rpim(I) all: 0.15 / Rrim(I) all: 0.561 / Net I/σ(I): 5.5
Reflection shellResolution: 2.982→3.28 Å / Redundancy: 14 % / Rmerge(I) obs: 2.309 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2764 / CC1/2: 0.544 / Rpim(I) all: 0.639 / Rrim(I) all: 2.396 / % possible all: 64.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→85.84 Å / SU ML: 0.3498 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.276 5458 9.89 %
Rwork0.2311 49709 -
obs0.2355 55167 69.22 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.11 Å2
Refinement stepCycle: LAST / Resolution: 2.98→85.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19049 0 0 3 19052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001619498
X-RAY DIFFRACTIONf_angle_d0.426226490
X-RAY DIFFRACTIONf_chiral_restr0.0372867
X-RAY DIFFRACTIONf_plane_restr0.00363472
X-RAY DIFFRACTIONf_dihedral_angle_d12.25857058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.010.486840.332733X-RAY DIFFRACTION1.41
3.01-3.050.4317110.429770X-RAY DIFFRACTION3.19
3.05-3.080.5085290.3753192X-RAY DIFFRACTION8.43
3.08-3.120.3426290.3538241X-RAY DIFFRACTION10.65
3.12-3.160.4421270.3244377X-RAY DIFFRACTION15.19
3.16-3.210.3151510.3166444X-RAY DIFFRACTION19.16
3.21-3.250.4133680.3148662X-RAY DIFFRACTION27.73
3.25-3.30.41121010.3237918X-RAY DIFFRACTION38.95
3.3-3.350.38441290.30561128X-RAY DIFFRACTION48.12
3.35-3.410.36721360.30661294X-RAY DIFFRACTION53.48
3.41-3.470.38351490.28471354X-RAY DIFFRACTION58.05
3.47-3.530.29121580.29431537X-RAY DIFFRACTION64.01
3.53-3.60.37042040.28231684X-RAY DIFFRACTION71.3
3.6-3.670.3381970.26541851X-RAY DIFFRACTION78.08
3.67-3.750.29041990.25932003X-RAY DIFFRACTION83.73
3.75-3.840.29942280.23772211X-RAY DIFFRACTION92.6
3.84-3.940.29812680.23182331X-RAY DIFFRACTION97.2
3.94-4.040.28882760.23892322X-RAY DIFFRACTION98.93
4.04-4.160.27332540.23192383X-RAY DIFFRACTION99.66
4.16-4.290.26122510.20982400X-RAY DIFFRACTION99.85
4.3-4.450.22562590.19112400X-RAY DIFFRACTION99.85
4.45-4.630.2582940.19952351X-RAY DIFFRACTION99.81
4.63-4.840.22972730.18972382X-RAY DIFFRACTION99.77
4.84-5.090.23972510.19782411X-RAY DIFFRACTION99.89
5.09-5.410.26092910.21522397X-RAY DIFFRACTION99.93
5.41-5.830.29922720.22172385X-RAY DIFFRACTION99.92
5.83-6.420.272660.22412443X-RAY DIFFRACTION99.82
6.42-7.340.24042670.22542445X-RAY DIFFRACTION99.74
7.34-9.250.20622800.20312457X-RAY DIFFRACTION99.93
9.25-85.840.24312360.22362603X-RAY DIFFRACTION98.41

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