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- PDB-2r14: Structure of morphinone reductase in complex with tetrahydroNAD -

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Basic information

Entry
Database: PDB / ID: 2r14
TitleStructure of morphinone reductase in complex with tetrahydroNAD
ComponentsMorphinone reductase
KeywordsFLAVOPROTEIN / H-tunnelling / NADH / morphinone reductase / hydride transfer / OXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / FMN binding / 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 / Chem-TXD / Morphinone reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCostello, C.L. / Scrutton, N.S. / Leys, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Mutagenesis of morphinone reductase induces multiple reactive configurations and identifies potential ambiguity in kinetic analysis of enzyme tunneling mechanisms.
Authors: Pudney, C.R. / Hay, S. / Pang, J. / Costello, C. / Leys, D. / Sutcliffe, M.J. / Scrutton, N.S.
History
DepositionAug 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: 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

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Assembly

Deposited unit
A: Morphinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4153
Polymers41,2911
Non-polymers1,1242
Water12,322684
1
A: Morphinone reductase
hetero molecules

A: Morphinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8296
Polymers82,5822
Non-polymers2,2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Buried area7210 Å2
ΔGint-18 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.271, 118.888, 180.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-639-

HOH

21A-713-

HOH

31A-718-

HOH

41A-755-

HOH

51A-926-

HOH

61A-1023-

HOH

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Components

#1: Protein Morphinone reductase


Mass: 41290.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: morB / Production host: Escherichia coli (E. coli) / References: UniProt: Q51990
#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-TXD / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE


Mass: 667.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H31N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5M ammonium sulphate, 0.1M Hepes, saturating tetrahydroNAD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 123781 / Num. obs: 123781 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.1
Reflection shellResolution: 1.3→1.34 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.3 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→12 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.996 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.053 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18063 4985 5 %RANDOM
Rwork0.1557 ---
all0.1557 94812 --
obs0.15696 94812 89.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20 Å2
2--5.23 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 78 684 3569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222962
X-RAY DIFFRACTIONr_bond_other_d0.0020.022608
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9944044
X-RAY DIFFRACTIONr_angle_other_deg0.97536036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67623.197147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48915424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.921529
X-RAY DIFFRACTIONr_chiral_restr0.1070.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
X-RAY DIFFRACTIONr_nbd_refined0.2120.2676
X-RAY DIFFRACTIONr_nbd_other0.210.22819
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21463
X-RAY DIFFRACTIONr_nbtor_other0.0840.21537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2456
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.236
X-RAY DIFFRACTIONr_mcbond_it1.8331.52301
X-RAY DIFFRACTIONr_mcbond_other1.1931.5738
X-RAY DIFFRACTIONr_mcangle_it2.26722880
X-RAY DIFFRACTIONr_scbond_it3.43731374
X-RAY DIFFRACTIONr_scangle_it4.5584.51164
X-RAY DIFFRACTIONr_rigid_bond_restr1.87536740
X-RAY DIFFRACTIONr_sphericity_free9.7383684
X-RAY DIFFRACTIONr_sphericity_bonded8.68335493
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 357 -
Rwork0.269 6881 -
obs--85.4 %

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