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- PDB-1vyr: Structure of pentaerythritol tetranitrate reductase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1vyr
TitleStructure of pentaerythritol tetranitrate reductase complexed with picric acid
ComponentsPENTAERYTHRITOL TETRANITRATE REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / EXPLOSIVE DEGRADATION / STEROID BINDING
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / cytosol
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 / PICRIC ACID / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesENTEROBACTER CLOACAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsBarna, T. / Moody, P.C.E.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Atomic Resolution Structures and Solution Behavior of Enzyme-Substrate Complexes of Enterobacter Cloacae Pb2 Pentaerythritol Tetranitrate Reductase: Multiple Conformational States and ...Title: Atomic Resolution Structures and Solution Behavior of Enzyme-Substrate Complexes of Enterobacter Cloacae Pb2 Pentaerythritol Tetranitrate Reductase: Multiple Conformational States and Implications for the Mechanism of Nitroaromatic Explosive Degradation
Authors: Khan, H. / Barna, T. / Harris, R. / Bruce, N. / Barsukov, I. / Munro, A. / Moody, P.C.E. / Scrutton, N.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of Pentaerythritol Tetranitrate Reductase: "Flipped" Binding Geometries for Steroid Substrates in Different Redox States of the Enzyme
Authors: Barna, T.M. / Khan, H. / Bruce, N.C. / Barsukov, I. / Scrutton, N.S. / Moody, P.C.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallisation and Preliminary Diffraction Studies of Pentaerythritol Reductase from Enterobacter Cloacae Pb2
Authors: Moody, P.C.E. / Shikotra, N. / French, C.E. / Bruce, N.C. / Scrutton, N.S.
History
DepositionMay 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Aug 13, 2014Group: Atomic model / Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PENTAERYTHRITOL TETRANITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0893
Polymers39,4041
Non-polymers6852
Water14,124784
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.979, 69.058, 89.121
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 PENTAERYTHRITOL TETRANITRATE REDUCTASE


Mass: 39404.000 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-365
Source method: isolated from a genetically manipulated source
Details: 2,4,6 TRINITROPHENOL IS BOUND IN THE ACTIVE SITE / Source: (gene. exp.) ENTEROBACTER CLOACAE (bacteria) / Description: NCBI U68759. RECOMBINANT / Plasmid: PONR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P71278
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-TNF / PICRIC ACID / 2,4,6-TRINITROPHENOL


Mass: 229.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3N3O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growpH: 6.2 / Details: pH 6.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 12, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 0.9→10 Å / Num. obs: 68596 / % possible obs: 94.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 29.7
Reflection shellResolution: 0.9→0.94 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4 / % possible all: 65.7

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GVS

1gvs


Resolution: 0.9→10 Å / Num. parameters: 33636 / Num. restraintsaints: 40616 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1398 -5 %RANDOM
all0.1162 233224 --
obs0.1 -94.8 %-
Refine analyzeNum. disordered residues: 32 / Occupancy sum hydrogen: 2459.36 / Occupancy sum non hydrogen: 3575.74
Refinement stepCycle: LAST / Resolution: 0.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 47 784 3604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.041
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0316
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.058
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.112

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