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- PDB-1h51: Oxidised Pentaerythritol Tetranitrate Reductase (SCN complex) -

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Basic information

Entry
Database: PDB / ID: 1h51
TitleOxidised Pentaerythritol Tetranitrate Reductase (SCN complex)
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 / THIOCYANATE ION / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesENTEROBACTER CLOACAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBarna, T. / Moody, P.C.E.
Citation
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.E.
#1: 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 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 "A2" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "A2" 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)39,9183
Polymers39,4041
Non-polymers5142
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.500, 68.520, 88.230
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: THIOCYANATE IS BOUND IN THE ACTIVE SITE / Source: (gene. exp.) ENTEROBACTER CLOACAE (bacteria) / Strain: PB2 / 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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.3 Å3/Da / Density % sol: 38 %
Crystal growpH: 6.2
Details: 25% PEG 3000, 0.05M SODIUM THIOCYANATE, 0.1M SODIUM CACODYLATE, 17% ISOPROPANOL PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 51016 / % possible obs: 93.7 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 24.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
ARP/wARPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYA

1oya


Resolution: 1.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.207 -5 %RANDOM
Rwork0.192 ---
obs0.192 51016 91.7 %-
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 34 476 3277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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