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- PDB-3bm2: Crystal structure of a minimal nitroreductase ydjA from Escherich... -

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Basic information

Entry
Database: PDB / ID: 3bm2
TitleCrystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor
ComponentsProtein ydjA
KeywordsOXIDOREDUCTASE / ydja / nitroreductase
Function / homology
Function and homology information


Oxidoreductases / FMN binding / oxidoreductase activity / protein homodimerization activity / cytosol
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
Putative NAD(P)H nitroreductase YdjA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsChoi, J.W. / Kim, J.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor
Authors: Choi, J.-W. / Lee, J. / Nishi, K. / Kim, Y.-S. / Jung, C.-H. / Kim, J.-S.
History
DepositionDec 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ydjA
B: Protein ydjA


Theoretical massNumber of molelcules
Total (without water)41,3732
Polymers41,3732
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-45.6 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.549, 129.280, 36.880
Angle α, β, γ (deg.)90.00, 103.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein ydjA / nitroreductase


Mass: 20686.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ydjA / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P0ACY1, 6,7-dihydropteridine reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20%(w/v) polyethyleneglycol 1000, 0.2M lithium sulfate, 0.1M phosphate-citrate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 15, 2007 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 26993 / Num. obs: 26237 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.097
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Num. unique all: 2244 / Rsym value: 0.505 / % possible all: 83.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.44 Å / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2111 -RANDOM
Rwork0.2161 ---
obs0.2161 21380 92.1 %-
all-23213 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.199 Å20 Å2-4.298 Å2
2--7.793 Å20 Å2
3---9.406 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 0 273 2797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.05
LS refinement shellResolution: 2.1→2.12 Å /
RfactorNum. reflection
Rfree0.341 49
Rwork0.324 -
obs-428

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