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- PDB-2i7h: Crystal Structure of the Nitroreductase-like Family Protein from ... -

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Basic information

Entry
Database: PDB / ID: 2i7h
TitleCrystal Structure of the Nitroreductase-like Family Protein from Bacillus cereus
ComponentsNitroreductase-like family protein
KeywordsOXIDOREDUCTASE / alpha-beta / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Putative NAD(P)H nitroreductase YdjA-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Nitroreductase family
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKim, Y. / Li, H. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Nitroreductase-like Family Protein from Bacillus cereus
Authors: Kim, Y. / Li, H. / Moy, S. / Joachimiak, A.
History
DepositionAug 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitroreductase-like family protein
B: Nitroreductase-like family protein
C: Nitroreductase-like family protein
D: Nitroreductase-like family protein
E: Nitroreductase-like family protein
F: Nitroreductase-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,27617
Polymers130,7786
Non-polymers2,49811
Water16,177898
1
A: Nitroreductase-like family protein
B: Nitroreductase-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6976
Polymers43,5932
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-78 kcal/mol
Surface area16380 Å2
MethodPISA
2
C: Nitroreductase-like family protein
D: Nitroreductase-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7937
Polymers43,5932
Non-polymers1,2015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-100 kcal/mol
Surface area16220 Å2
MethodPISA
3
E: Nitroreductase-like family protein
F: Nitroreductase-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7854
Polymers43,5932
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-73 kcal/mol
Surface area17030 Å2
MethodPISA
4
A: Nitroreductase-like family protein
B: Nitroreductase-like family protein
C: Nitroreductase-like family protein
D: Nitroreductase-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,49113
Polymers87,1854
Non-polymers2,3069
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20780 Å2
ΔGint-197 kcal/mol
Surface area30390 Å2
MethodPISA
5
E: Nitroreductase-like family protein
F: Nitroreductase-like family protein
hetero molecules

E: Nitroreductase-like family protein
F: Nitroreductase-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5698
Polymers87,1854
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area16010 Å2
ΔGint-158 kcal/mol
Surface area32110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.719, 87.217, 81.189
Angle α, β, γ (deg.)90.00, 103.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nitroreductase-like family protein


Mass: 21796.299 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: DSM 31 / Gene: BC_0786 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81HL8
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 0.2M Ammonium sulfate, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 13, 2004 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.3→40.91 Å / Num. all: 74322 / Num. obs: 74322 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.66 / Num. unique all: 7348 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHARPphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→40.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.37 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.21254 7399 10.1 %RANDOM
Rwork0.17168 ---
all0.17581 66017 --
obs0.17581 66017 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.684 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20.34 Å2
2--0.97 Å20 Å2
3----2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9015 0 159 898 10072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210357
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.97714146
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40351315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54323.936503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.103151885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9821591
X-RAY DIFFRACTIONr_chiral_restr0.1060.21481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028062
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.25289
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.27199
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2934
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.2138
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7471.56340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.219210084
X-RAY DIFFRACTIONr_scbond_it2.34734728
X-RAY DIFFRACTIONr_scangle_it3.6854.54062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 518 -
Rwork0.224 4846 -
obs-4846 99.68 %
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)
10.811-0.1745-0.2230.75640.06381.3651-0.0145-0.02610.004-0.10930.0256-0.04030.00470.1474-0.0111-0.18770.01950.0065-0.2243-0.0094-0.213966.785261.123845.5324
20.92180.217-0.05890.95730.23141.2157-0.018-0.09190.03140.10160.02840.03980.05370.1405-0.0104-0.18330.00130.0021-0.2116-0.0109-0.190577.121869.87871.5231
31.2256-0.3382-0.23361.15960.09492.3091-0.0495-0.2244-0.02410.0720.03620.04160.0343-0.24080.0132-0.25420.03670.0206-0.15780.016-0.2644113.098321.723516.4707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 186
2X-RAY DIFFRACTION1B0 - 186
3X-RAY DIFFRACTION1A1001 - 1002
4X-RAY DIFFRACTION2C0 - 186
5X-RAY DIFFRACTION2D0 - 186
6X-RAY DIFFRACTION2A1003 - 1004
7X-RAY DIFFRACTION3E1 - 185
8X-RAY DIFFRACTION3F0 - 186
9X-RAY DIFFRACTION3A1005 - 1006

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