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- PDB-1gvo: STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE AND COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 1gvo
TitleSTRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE AND COMPLEXED WITH 2,4 DINITROPHENOL
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
2,4-DINITROPHENOL / FLAVIN MONONUCLEOTIDE / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesENTEROBACTER CLOACAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsBarna, T. / Moody, P.C.E.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Kinetic and Structural Basis of Reactivity of Pentaerythritol Tetranitrate Reductase with Nadph,2-Cyclohexenone Nitroesters and Nitroaromatic Explosives
Authors: Khan, H. / Harris, R. / Barna, T. / Craig, D. / Bruce, N. / 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
DepositionFeb 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2May 1, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
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

Downloads & links

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Assembly

Deposited unit
A: PENTAERYTHRITOL TETRANITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0443
Polymers39,4041
Non-polymers6402
Water14,736818
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.963, 69.094, 89.024
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
Source method: isolated from a genetically manipulated source
Details: 2,4 DINITROPHENOL 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-DNF / 2,4-DINITROPHENOL


Mass: 184.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 818 / 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: 44.67 %
Crystal growpH: 6.2 / Details: pH 6.20
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Barna, T.M., (2001) J. Mol. Biol., 310, 433. / pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %(w/v)PEG30001reservoir
20.1 Mcacodylic acid1reservoirpH6.2
317 %(v/v)isopropanol1reservoir
40.1 M1reservoirNaCl
50.1 Msodium acetate1reservoir
60.05 Msodium thiocyanate1reservoir

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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, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 68596 / % possible obs: 96.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 32.7
Reflection shellResolution: 1.38→1.47 Å / % possible all: 79
Reflection
*PLUS
Num. obs: 69990 / % possible obs: 97.8 % / Num. measured all: 301258

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H50

1h50


Resolution: 1.38→50 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3351 4.9 %RANDOM
Rwork0.175 ---
obs0.175 68596 96.2 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 12.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--1.13 Å20 Å2
3----0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 44 818 3630
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.231.5
X-RAY DIFFRACTIONc_mcangle_it0.412
X-RAY DIFFRACTIONc_scbond_it0.42
X-RAY DIFFRACTIONc_scangle_it0.612.5
LS refinement shellResolution: 1.38→1.47 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.211 502 5.3 %
Rwork0.212 8980 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FMN.PARWATER.TOP
X-RAY DIFFRACTION3ACE.PARDNF.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMFMN.TOP
Refinement
*PLUS
Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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