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- PDB-1h61: Structure of Pentaerythritol Tetranitrate Reductase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1h61
TitleStructure of Pentaerythritol Tetranitrate Reductase in complex with prednisone
ComponentsPENTAERYTHRITOL TETRANITRATE REDUCTASE
KeywordsOXIDOREDUCTASE / STEROID BINDING / FLAVOENZYME
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 / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesENTEROBACTER CLOACAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBarna, T.M. / Moody, P.C.E.
CitationJournal: 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.
History
DepositionJun 4, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 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 "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)40,2193
Polymers39,4041
Non-polymers8152
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.784, 69.478, 88.821
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: NON-COVALENTLY BOUND FLAVIN MONONUCLEOTIDE / Source: (gene. exp.) ENTEROBACTER CLOACAE (bacteria) / Strain: PB2 / Plasmid: PONR / 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-PDN / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / PREDNISONE / 1,4 PREGNADIENE-17ALPHA,21-DIOL-3,11,20-TRIONE / 1-CORTISONE / DEHYDROCORTISONE


Mass: 358.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 44.68 %
Crystal growpH: 6.5 / Details: PEG 2000, 0.1M CACODYLIC ACID, PH 6.5, 15% MEOH
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %(w/v)PEG30001reservoir
20.1 Mtrisodium citrate1reservoir
30.1 Mcacodylic acid1reservoirpH6.2
417 %(v/v)isopropanol1reservoir

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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 / Date: Jan 15, 2000 / 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: 1.4→100 Å / Num. obs: 69990 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 37.3
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 14 / % possible all: 94.6
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 972397 / Rmerge(I) obs: 0.053

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Processing

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

1oya


Resolution: 1.4→44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1275816.11 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3341 4.9 %RANDOM
Rwork0.198 ---
obs0.198 68177 97.4 %-
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--1.38 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.4→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 57 545 3380
Refine LS restraints
Refine-IDTypeDev ideal
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_d0.94
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
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 566 5.2 %
Rwork0.32 10336 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1FMN.PARFMN.TOP
X-RAY DIFFRACTION2PDN.PARPDN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 44 Å / Rfactor obs: 0.212 / Rfactor Rfree: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rwork: 0.32

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