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- PDB-3uog: Crystal structure of putative Alcohol dehydrogenase from Sinorhiz... -

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Basic information

Entry
Database: PDB / ID: 3uog
TitleCrystal structure of putative Alcohol dehydrogenase from Sinorhizobium meliloti 1021
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase
Similarity search - Function
: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alcohol dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti 1021 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of putative Alcohol dehydrogenase from Sinorhizobium meliloti 1021
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,6575
Polymers78,3692
Non-polymers2883
Water2,738152
1
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
hetero molecules

A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,31410
Polymers156,7384
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area12560 Å2
ΔGint-123 kcal/mol
Surface area49270 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-57 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.222, 102.396, 79.018
Angle α, β, γ (deg.)90.000, 118.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

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Components

#1: Protein Alcohol dehydrogenase


Mass: 39184.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Strain: 1021 / Gene: R02449, SMc01816 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q92MZ8, alcohol dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 91519 / % possible obs: 88 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.088 / Χ2: 1.086 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2420.79930420.928158.9
2.24-2.282.10.77733710.92164.5
2.28-2.322.20.736070.886169
2.32-2.372.20.64638720.915175
2.37-2.422.20.66240940.934179.4
2.42-2.482.20.56344380.912184.9
2.48-2.542.20.47846210.94189
2.54-2.612.20.42548220.962192.7
2.61-2.692.20.35448580.923193.9
2.69-2.772.20.27848180.987192.3
2.77-2.872.20.21148051.046193.2
2.87-2.992.30.17949181.169194.2
2.99-3.122.30.14949531.234194
3.12-3.292.30.11448561.34194
3.29-3.492.30.09649441.493194.9
3.49-3.762.30.08650601.362196.8
3.76-4.142.30.07950771.386197.8
4.14-4.742.30.06750681.253197.6
4.74-5.972.30.05351350.965198.8
5.97-502.40.04351600.792199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EIH

2eih


Resolution: 2.2→19.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2495 / WRfactor Rwork: 0.2076 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7819 / SU B: 14.358 / SU ML: 0.175 / SU R Cruickshank DPI: 0.2167 / SU Rfree: 0.1925 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 2519 5.1 %RANDOM
Rwork0.2068 ---
obs0.209 49177 93.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 181.23 Å2 / Biso mean: 58.4455 Å2 / Biso min: 30.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.02 Å2
2--0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5115 0 15 152 5282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195266
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9857163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7645686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66222.657207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.03415805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0411545
X-RAY DIFFRACTIONr_chiral_restr0.0940.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213985
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 119 -
Rwork0.32 2346 -
all-2465 -
obs--64.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4657-0.08090.59431.02450.15161.6046-0.1587-0.21480.31490.0979-0.11050.0163-0.1225-0.16560.26920.1330.00280.03250.1367-0.1010.146613.733214.7541-14.425
21.32110.31180.69470.97430.81231.64710.1198-0.138-0.0359-0.0486-0.24440.40420.1629-0.19170.12460.2738-0.02980.04880.2302-0.10130.2794-0.7254-14.732-41.5051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 340
2X-RAY DIFFRACTION2B0 - 340

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