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- PDB-3kft: Crystal structure of Pentaerythritol Tetranitrate Reductase compl... -

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Basic information

Entry
Database: PDB / ID: 3kft
TitleCrystal structure of Pentaerythritol Tetranitrate Reductase complex with 1,4,5,6-tetrahydro NADH
ComponentsPentaerythritol tetranitrate reductase
KeywordsOXIDOREDUCTASE / NADH:flavin oxidoreductase / NADH oxidase family
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPudney, C.R. / Levy, C.W. / Leys, D. / Scrutton, N.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Evidence to support the hypothesis that promoting vibrations enhance the rate of an enzyme catalyzed H-tunneling reaction.
Authors: Pudney, C.R. / Hay, S. / Levy, C. / Pang, J. / Sutcliffe, M.J. / Leys, D. / Scrutton, N.S.
History
DepositionOct 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pentaerythritol tetranitrate reductase
B: Pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0486
Polymers78,8082
Non-polymers2,2404
Water10,269570
1
A: Pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5243
Polymers39,4041
Non-polymers1,1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5243
Polymers39,4041
Non-polymers1,1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.150, 57.150, 410.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Pentaerythritol tetranitrate reductase


Mass: 39404.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: onr / Production host: Escherichia coli (E. coli) / References: UniProt: P71278
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Magnesium chloride, 0.1M Tris HCl pH 8.5 & 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0698 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0698 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 43135 / Num. obs: 43135 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.69
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.77 / Num. unique all: 6646 / % possible all: 94.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.112 Å / SU ML: 0.27 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 2169 5.03 %
Rwork0.1626 --
obs0.1657 43133 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.641 Å2 / ksol: 0.317 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→40.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5493 0 150 570 6213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145771
X-RAY DIFFRACTIONf_angle_d1.5227871
X-RAY DIFFRACTIONf_dihedral_angle_d21.3732106
X-RAY DIFFRACTIONf_chiral_restr0.094862
X-RAY DIFFRACTIONf_plane_restr0.0071030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.14910.31321550.21912523X-RAY DIFFRACTION93
2.1491-2.20290.3281280.21822706X-RAY DIFFRACTION95
2.2029-2.26240.30071470.21982610X-RAY DIFFRACTION96
2.2624-2.3290.29831550.20592663X-RAY DIFFRACTION97
2.329-2.40420.25961580.18762728X-RAY DIFFRACTION98
2.4042-2.49010.29861350.18012770X-RAY DIFFRACTION99
2.4901-2.58980.28431370.18422735X-RAY DIFFRACTION99
2.5898-2.70760.23751350.18552789X-RAY DIFFRACTION99
2.7076-2.85030.26571440.17582781X-RAY DIFFRACTION100
2.8503-3.02880.26151590.17882760X-RAY DIFFRACTION100
3.0288-3.26260.24721500.16812737X-RAY DIFFRACTION100
3.2626-3.59070.21391450.15782821X-RAY DIFFRACTION100
3.5907-4.10990.17981370.13962797X-RAY DIFFRACTION100
4.1099-5.17630.15851630.11972762X-RAY DIFFRACTION100
5.1763-40.11960.14661210.1332782X-RAY DIFFRACTION99

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