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- PDB-4jip: Crystal structure of glycerol trinitrate reductase NerA from Agro... -

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Basic information

Entry
Database: PDB / ID: 4jip
TitleCrystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde
ComponentsGTN Reductase
KeywordsOXIDOREDUCTASE / TIM-Barrel / ene-reductase
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / P-HYDROXYBENZALDEHYDE / GTN Reductase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsOberdorfer, G. / Gruber, K.
CitationJournal: Chembiochem / Year: 2013
Title: The Structure of Glycerol Trinitrate Reductase NerA from Agrobacterium radiobacter Reveals the Molecular Reason for Nitro- and Ene-Reductase Activity in OYE Homologues.
Authors: Oberdorfer, G. / Binter, A. / Wallner, S. / Durchschein, K. / Hall, M. / Faber, K. / Macheroux, P. / Gruber, K.
History
DepositionMar 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: GTN Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1463
Polymers40,5681
Non-polymers5782
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.910, 68.280, 90.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GTN Reductase


Mass: 40567.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: nerA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31246
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-HBA / P-HYDROXYBENZALDEHYDE / 4-Hydroxybenzaldehyde


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, 25% w/v polyethylene glycol 3,350, pH 6.0, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2010
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→54.41 Å / Num. all: 17038 / Num. obs: 16687 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2252 / Rsym value: 0.309 / % possible all: 93.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4jic

4jic


Resolution: 2.29→45.03 Å / SU ML: 0.63 / σ(F): 1.36 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 839 5.04 %RANDOM
Rwork0.1943 ---
obs0.1965 16644 97.7 %-
all-17038 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.995 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.44 Å2-0 Å2-0 Å2
2---2.3405 Å20 Å2
3----6.5701 Å2
Refinement stepCycle: LAST / Resolution: 2.29→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 40 218 3057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062930
X-RAY DIFFRACTIONf_angle_d0.9343995
X-RAY DIFFRACTIONf_dihedral_angle_d14.3331067
X-RAY DIFFRACTIONf_chiral_restr0.066427
X-RAY DIFFRACTIONf_plane_restr0.005537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.42830.26161420.22012427X-RAY DIFFRACTION92
2.4283-2.61580.27241440.20432511X-RAY DIFFRACTION95
2.6158-2.8790.2531460.1982616X-RAY DIFFRACTION99
2.879-3.29550.24011230.1932689X-RAY DIFFRACTION100
3.2955-4.15150.2211510.16972710X-RAY DIFFRACTION100
4.1515-45.03880.22031330.20262852X-RAY DIFFRACTION100

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