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- PDB-3qdl: Crystal structure of RdxA from Helicobacter pyroli -

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Basic information

Entry
Database: PDB / ID: 3qdl
TitleCrystal structure of RdxA from Helicobacter pyroli
ComponentsOxygen-insensitive NADPH nitroreductase
KeywordsOXIDOREDUCTASE / oxygen-insensitive NAD(P)H nitroreductase
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / response to antibiotic
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Oxygen-insensitive NADPH nitroreductase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsRojas, A.L. / Martinez-Julvez, M. / Olekhnovich, I.N. / Hoffman, P.S. / Sancho, J.
CitationJournal: Febs J. / Year: 2012
Title: Structure of RdxA--an oxygen-insensitive nitroreductase essential for metronidazole activation in Helicobacter pylori.
Authors: Martinez-Julvez, M. / Rojas, A.L. / Olekhnovich, I. / Espinosa Angarica, V. / Hoffman, P.S. / Sancho, J.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Jan 30, 2013Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxygen-insensitive NADPH nitroreductase
B: Oxygen-insensitive NADPH nitroreductase
C: Oxygen-insensitive NADPH nitroreductase
D: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,41410
Polymers96,4044
Non-polymers2,0106
Water3,063170
1
A: Oxygen-insensitive NADPH nitroreductase
B: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2075
Polymers48,2022
Non-polymers1,0053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-52 kcal/mol
Surface area15720 Å2
MethodPISA
2
C: Oxygen-insensitive NADPH nitroreductase
D: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2075
Polymers48,2022
Non-polymers1,0053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-49 kcal/mol
Surface area15690 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19740 Å2
ΔGint-115 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.440, 49.440, 304.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Oxygen-insensitive NADPH nitroreductase


Mass: 24101.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: rdxA, HP_0954 / Plasmid: pET15brdxA5 / Production host: Escherichia coli (E. coli) / References: UniProt: O25608
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25 % PEG 3350, 0.1 M Bis-Tris, 0.2 M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-210.8726
SYNCHROTRONESRF BM1420.97625
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDFeb 19, 2010
MARMOSAIC 325 mm CCD2CCDApr 10, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111) monochromatorSINGLE WAVELENGTHMx-ray1
2Si (111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
20.976251
ReflectionRedundancy: 5.5 % / Av σ(I) over netI: 3.6 / Number: 266704 / Rsym value: 0.145 / D res high: 2 Å / D res low: 76.12 Å / Num. obs: 48813 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.3238.3897.910.0860.0865.7
4.476.3299.110.1140.1145.6
3.654.4799.310.1310.1315.5
3.163.6599.610.1340.1345.5
2.833.1699.710.1470.1475.6
2.582.8399.810.1690.1695.5
2.392.5899.910.1830.1835.5
2.242.3910010.2050.2055.4
2.112.2410010.2420.2425.4
22.1110010.320.325.3
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.499
11K, H, -L20.501
ReflectionResolution: 2→76.12 Å / Num. all: 48813 / Num. obs: 48813 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rsym value: 0.145 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.115.30.322.43755271150.32100
2.11-2.245.40.2423.13677867850.242100
2.24-2.395.40.2053.63431563310.205100
2.39-2.585.50.1833.93238259340.18399.9
2.58-2.835.50.1694.12972654140.16999.8
2.83-3.165.60.1474.72726849110.14799.7
3.16-3.655.50.1344.82395643170.13499.6
3.65-4.475.50.1314.82032636660.13199.3
4.47-6.325.60.1145.11573128110.11499.1
6.32-38.3835.70.0866.6867015290.08697.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.38 Å
Translation2.5 Å38.38 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1icr

1icr


Resolution: 2→76.12 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2337 / WRfactor Rwork: 0.1992 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8542 / SU B: 2.964 / SU ML: 0.083 / SU R Cruickshank DPI: 0.0403 / SU Rfree: 0.0335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 2511 5.1 %RANDOM
Rwork0.1881 ---
obs0.1898 48807 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.8 Å2 / Biso mean: 19.935 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å20 Å2
2---0.36 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2→76.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5444 0 136 170 5750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225672
X-RAY DIFFRACTIONr_angle_refined_deg0.9152.0027630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9155676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98224.359234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.007151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.341532
X-RAY DIFFRACTIONr_chiral_restr0.0610.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214068
X-RAY DIFFRACTIONr_mcbond_it0.281.53416
X-RAY DIFFRACTIONr_mcangle_it0.50925500
X-RAY DIFFRACTIONr_scbond_it0.57632256
X-RAY DIFFRACTIONr_scangle_it0.9334.52130
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 167 -
Rwork0.19 3435 -
all-3602 -
obs--98.39 %

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