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- PDB-4bmn: apo structure of short-chain alcohol dehydrogenase from Ralstonia... -

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Basic information

Entry
Database: PDB / ID: 4bmn
Titleapo structure of short-chain alcohol dehydrogenase from Ralstonia sp. DSM 6428
ComponentsALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
KeywordsOXIDOREDUCTASE / KRED / BIOCATALYST
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
Alclohol dehydrogenase/short-chain dehydrogenase
Similarity search - Component
Biological speciesRALSTONIA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMan, H. / Kulig, J. / Rother, D. / Grogan, G.
CitationJournal: Top.Catal. / Year: 2014
Title: Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium Spp. Reveal the Molecular Basis for Their Recognition of 'Bulky-Bulky' Ketones
Authors: Man, H. / Kedziora, K. / Kulig, J. / Frank, A. / Lavandera, I. / Gotor-Fernandez, V. / Rother, D. / Hart, S. / Turkenburg, J.P. / Grogan, G.
History
DepositionMay 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
B: ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
C: ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
D: ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,11913
Polymers108,4594
Non-polymers6609
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19890 Å2
ΔGint-68.5 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.480, 52.510, 151.470
Angle α, β, γ (deg.)90.00, 116.57, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7713, -0.5759, 0.271), (-0.5692, 0.4336, -0.6986), (0.2848, -0.6931, -0.6622)38.07, 40.76, 52.76
2given(-0.9587, 0.1399, 0.2478), (0.1347, -0.5438, 0.8283), (0.2506, 0.8274, 0.5025)39.64, -23, 6.105
3given(0.7291, 0.4375, -0.5268), (0.4375, -0.8895, -0.1322), (-0.5264, -0.1341, -0.8396)22.15, 3.724, 75.96

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Components

#1: Protein
ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE / ALCOHOL DEHYDROGENASE


Mass: 27114.740 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA SP. (bacteria) / Strain: DSMZ 6428 / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0IR58, alcohol dehydrogenase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O
Sequence details'QGPA' AT THE BEGINNING ARE PART OF A LINKING SEQUENCE TO AN N-TERMINAL HIS-TAG

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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: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 7
Details: 0.1M BIS-TRIS PROPANE PH 7.0 CONTAINING 20% (W/V) PEG 3350 AND 0.02 M SODIUM-POTASSIUM PHOSPHATE. THE PROTEIN CONCENTRATION WAS 24 MG ML-1.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.52→60.86 Å / Num. obs: 149646 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.6
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.9 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FGS

4fgs


Resolution: 1.5→60.86 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.26 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18784 7501 5 %RANDOM
Rwork0.15812 ---
obs0.15962 141654 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.997 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.12 Å2
2--1.87 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6877 0 43 847 7767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0197071
X-RAY DIFFRACTIONr_bond_other_d0.0110.027024
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9749589
X-RAY DIFFRACTIONr_angle_other_deg1.683316015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7122.804271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.088151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3061565
X-RAY DIFFRACTIONr_chiral_restr0.1310.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028073
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021565
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_it2.1241.9793750
X-RAY DIFFRACTIONr_mcbond_other2.1231.9793748
X-RAY DIFFRACTIONr_mcangle_it2.882.9624686
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0912.263321
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 561 -
Rwork0.213 10230 -
obs--95.97 %

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