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- PDB-1ywq: Crystal structure of a nitroreductase family protein from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 1ywq
TitleCrystal structure of a nitroreductase family protein from Bacillus cereus ATCC 14579
ComponentsNitroreductase family protein
KeywordsOXIDOREDUCTASE / Bacillus cereus / nitroreductase family protein / FMN / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


cellular response to oxidative stress / oxidoreductase activity / nucleotide binding / cytoplasm
Similarity search - Function
Nitroreductase Frm2/Hbn1-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Nitroreductase family protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMidwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a nitroreductase family protein from Bacillus cereus ATCC 14579
Authors: Zhang, R. / Li, H. / Collart, F. / Moy, S. / Joachimiak, A.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3062
Polymers22,8501
Non-polymers4561
Water1,29772
1
A: Nitroreductase family protein
hetero molecules

A: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6134
Polymers45,7002
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7850 Å2
ΔGint-45 kcal/mol
Surface area16580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.940, 80.940, 91.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThis protein existed as dimer. The second part of the biological assembly is generated by the operation: -x+y, -x, z+2/3

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Components

#1: Protein Nitroreductase family protein


Mass: 22849.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: ATCC 14579 / DSM 31 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81EW9
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.769 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.8M Na/K Phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 19, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 30056 / Num. obs: 30026 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 22.74
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.41 / Num. unique all: 3007 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→38.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 374962.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1393 4.9 %RANDOM
Rwork0.205 ---
all0.21 30026 --
obs0.205 28495 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7973 Å2 / ksol: 0.372893 e/Å3
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å23.86 Å20 Å2
2--1.83 Å20 Å2
3----3.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 31 72 1703
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 236 5.5 %
Rwork0.329 4044 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4FMN.PARAM

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