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- PDB-1h62: Structure of Pentaerythritol tetranitrate reductase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1h62
TitleStructure of Pentaerythritol tetranitrate reductase in complex with 1,4-androstadien-3,17-dione
ComponentsPENTAERYTHRITOL TETRANITRATE REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / STEROID BINDING
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
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
ANDROSTA-1,4-DIENE-3,17-DIONE / FLAVIN MONONUCLEOTIDE / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesENTEROBACTER CLOACAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2May 11, 2016Group: Structure summary
Revision 1.3May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)40,1453
Polymers39,4041
Non-polymers7412
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.709, 69.013, 88.708
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: PONR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P71278
#2: Chemical ChemComp-ANB / ANDROSTA-1,4-DIENE-3,17-DIONE / Boldione


Mass: 284.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24O2 / Comment: hormone*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 6.5 / Details: PEG 3000, 0.1M CACODYLIC ACID, 15% MEOH PH 6.8
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 FILTERS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 21069 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.5 / % possible all: 94.6
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 28269 / Num. measured all: 529105 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Rmerge(I) obs: 0.382

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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: 1.9→100 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1362424.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1223 4.7 %RANDOM
Rwork0.194 ---
obs0.194 25805 91.7 %-
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å20 Å20 Å2
2--3.41 Å20 Å2
3----0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 52 484 3314
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_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
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: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 196 4.9 %
Rwork0.284 3818 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1FMN.PARFMN.TOP
X-RAY DIFFRACTION2AND.PARAND.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / Rfactor obs: 0.201 / Rfactor Rfree: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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