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- PDB-3ak4: Crystal structure of NADH-dependent quinuclidinone reductase from... -

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Basic information

Entry
Database: PDB / ID: 3ak4
TitleCrystal structure of NADH-dependent quinuclidinone reductase from agrobacterium tumefaciens
ComponentsNADH-dependent quinuclidinone reductase
KeywordsOXIDOREDUCTASE / SDR / 3-QUINUCLIDINONE / (R)-3-QUINUCLIDINOL / CHIRAL ALCOHOL / CARBONYL REDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / quinone binding / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH-dependent quinuclidinone reductase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiyakawa, T. / Kataoka, M. / Takeshita, D. / Nomoto, F. / Nagata, K. / Shimizu, S. / Tanokura, M.
CitationJournal: To be Published
Title: Crystal structure of NADH-dependent quinuclidinone reductase from Agrobacterium tumefaciens
Authors: Miyakawa, T. / Kataoka, M. / Takeshita, D. / Nomoto, F. / Nagata, K. / Shimizu, S. / Tanokura, M.
History
DepositionJul 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH-dependent quinuclidinone reductase
B: NADH-dependent quinuclidinone reductase
C: NADH-dependent quinuclidinone reductase
D: NADH-dependent quinuclidinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0088
Polymers110,3544
Non-polymers2,6544
Water14,772820
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-84 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.550, 127.300, 62.480
Angle α, β, γ (deg.)90.00, 110.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NADH-dependent quinuclidinone reductase


Mass: 27588.557 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: G1K3P5*PLUS
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 820 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THREE N-TERMINAL ...THE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THREE N-TERMINAL RESIDUES ARE EXPRESSION TAGS.

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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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24% PEG3350, 100MM HEPES, 200MM AMMONIUM ACETATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 3, 2008
RadiationMonochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 61144 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rsym value: 0.045 / Net I/σ(I): 20.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 7.5 / Num. unique all: 26076 / Rsym value: 0.15 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.3refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GEG

1geg


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.289 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3081 5 %RANDOM
Rwork0.149 ---
obs0.151 58030 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å2-0.01 Å2
2---0.34 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 176 820 8592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227900
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.97710744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28751028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96224.051316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.417151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1241556
X-RAY DIFFRACTIONr_chiral_restr0.1020.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025916
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.23581
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2870.25349
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2536
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8641.55313
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17528092
X-RAY DIFFRACTIONr_scbond_it2.21633061
X-RAY DIFFRACTIONr_scangle_it3.2874.52652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 195 -
Rwork0.234 3922 -
obs--90.74 %

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