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- PDB-1vys: STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE W102Y MUTANT ... -

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Basic information

Entry
Database: PDB / ID: 1vys
TitleSTRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE W102Y MUTANT AND 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: 1.8 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: Crystallization and Preliminary Diffraction Studies of Pentaerythritol Tetranitrate 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 1.0May 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2Apr 24, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 1.4Dec 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 "XB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XB" 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
X: PENTAERYTHRITOL TETRANITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0663
Polymers39,3811
Non-polymers6852
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.591, 68.330, 88.603
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: 39380.965 Da / Num. of mol.: 1 / Mutation: YES
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.: 604 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN X, TRP 103 TO TYR

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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: 2.18 Å3/Da / Density % sol: 43.45 %
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, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29340 / % possible obs: 88.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.2 / % possible all: 92.7

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Processing

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

1gvs


Resolution: 1.8→34.92 Å / SU B: 2.467 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1404 4.9 %RANDOM
Rwork0.1421 ---
obs0.14495 27293 88.21 %-
Displacement parametersBiso mean: 12.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 47 604 3404

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