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- PDB-2amj: Crystal Structure of Modulator of Drug Activity B from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 2amj
TitleCrystal Structure of Modulator of Drug Activity B from Escherichia coli O157:H7
ComponentsModulator of drug activity B
KeywordsOXIDOREDUCTASE / menadione / DT-diaphorase / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / cytoplasm
Similarity search - Function
Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADPH:quinone oxidoreductase MdaB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsAdams, M.A. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Modulator of drug activity B from Escherichia coli: crystal structure of a prokaryotic homologue of DT-diaphorase.
Authors: Adams, M.A. / Jia, Z.
History
DepositionAug 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Remark 999SEQUENCE Residue 1 in chains A, B, C and D is a modified methionine (MSE) and is a cloning artifact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Modulator of drug activity B
B: Modulator of drug activity B
C: Modulator of drug activity B
D: Modulator of drug activity B


Theoretical massNumber of molelcules
Total (without water)93,8014
Polymers93,8014
Non-polymers00
Water10,557586
1
A: Modulator of drug activity B
B: Modulator of drug activity B


Theoretical massNumber of molelcules
Total (without water)46,9012
Polymers46,9012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-23 kcal/mol
Surface area15110 Å2
MethodPISA
2
C: Modulator of drug activity B
D: Modulator of drug activity B


Theoretical massNumber of molelcules
Total (without water)46,9012
Polymers46,9012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-26 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.056, 86.510, 82.667
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Modulator of drug activity B


Mass: 23450.365 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: mdaB, mda66 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEY7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.2 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / pH: 8.5
Details: Magnesium Chloride, Tris HCl, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298 K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2004
RadiationMonochromator: CHANNEL-CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→46 Å / Num. obs: 61582 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXmodel building
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→46 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3138 4.5 %RANDOM
Rwork0.233 ---
obs0.233 61582 --
all-69035 --
Displacement parametersBiso mean: 38.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.788 Å20 Å22.255 Å2
2--4.878 Å20 Å2
3----8.666 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 0 586 6348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.57
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3819 -2.5 %
Rwork0.3762 4916 -
obs--0.72 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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