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- PDB-6ihh: Crystal structure of RasADH F12 from Ralstonia.sp in complex with... -

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Basic information

Entry
Database: PDB / ID: 6ihh
TitleCrystal structure of RasADH F12 from Ralstonia.sp in complex with NADPH and A6O
ComponentsAlclohol dehydrogenase
KeywordsHYDROLASE/INHIBITOR / OXIDOREDUCTASE / KRED / BIOCATALYST / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / nucleotide binding
Similarity search - Function
PKS_KR / 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
Chem-A6O / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Alclohol dehydrogenase/short-chain dehydrogenase
Similarity search - Component
Biological speciesRalstonia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, H.L. / Chen, X. / Liu, W.D. / Wu, Q.Q. / Zhu, D.M.
CitationJournal: Nat Catal / Year: 2019
Title: Efficient reductive desymmetrization of bulky 1,3-cyclodiketones enabled by structure-guided directed evolution of a carbonyl reductase.
Authors: Chen, X. / Zhang, H. / Ma, M.S. / Liu, W. / Li, J. / Feng, J. / Liu, X. / Osuna, S. / Guo, R.T. / Wu, Q. / Zhu, D. / Ma, Y.
History
DepositionSep 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alclohol dehydrogenase
B: Alclohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0645
Polymers53,2622
Non-polymers1,8013
Water5,693316
1
A: Alclohol dehydrogenase
B: Alclohol dehydrogenase
hetero molecules

A: Alclohol dehydrogenase
B: Alclohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,12710
Polymers106,5254
Non-polymers3,6026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area17710 Å2
ΔGint-93 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.687, 118.687, 73.009
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Alclohol dehydrogenase


Mass: 26631.137 Da / Num. of mol.: 2 / Mutation: I91V,I187S,I188L,Q191N,F205A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia sp. (bacteria) / Plasmid: pET46Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C0IR58
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-A6O / (2R,3S)-2-ethyl-2-[(2E)-2-(6-methoxy-3,4-dihydro-2H-naphthalen-1-ylidene)ethyl]-3-oxidanyl-cyclopentan-1-one


Mass: 314.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.79 Å3/Da / Density % sol: 61.27 % / Mosaicity: 1 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium Sulfate, Bis-Tris, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 55225 / % possible obs: 99.4 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.033 / Rrim(I) all: 0.105 / Χ2: 1.279 / Net I/σ(I): 7 / Num. measured all: 565706
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.868.60.61351560.9470.2140.650.50193.6
1.86-1.9410.20.48554910.9770.1590.5110.573100
1.94-2.0310.40.37955350.9810.1230.3980.713100
2.03-2.1310.40.2954860.9870.0940.3050.839100
2.13-2.2710.40.2155350.9930.0680.2211.042100
2.27-2.4410.50.16955370.9940.0550.1781.177100
2.44-2.6910.50.13155450.9960.0420.1371.372100
2.69-3.0810.60.09855620.9970.0320.1031.722100
3.08-3.8710.50.07956020.9970.0260.0832.439100
3.87-2510.20.05657760.9980.0190.0592.151100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bms

4bms


Resolution: 1.8→24.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.416 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20393 2695 4.9 %RANDOM
Rwork0.16642 ---
obs0.16828 52388 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.053 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.6 Å20 Å2
2--1.2 Å2-0 Å2
3----3.9 Å2
Refinement stepCycle: 1 / Resolution: 1.8→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 119 316 4185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123923
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.6855340
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4415496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60220.8200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97115642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9491538
X-RAY DIFFRACTIONr_chiral_restr0.1110.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.022941
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.53.0791990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.7834.5882484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.8663.5811933
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.54260.92319410
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 176 -
Rwork0.245 3814 -
obs--99.28 %

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