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- PDB-3iv6: Crystal Structure of Putative Zn-dependent Alcohol Dehydrogenases... -

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Basic information

Entry
Database: PDB / ID: 3iv6
TitleCrystal Structure of Putative Zn-dependent Alcohol Dehydrogenases from Rhodobacter sphaeroides.
ComponentsPutative Zn-dependent Alcohol Dehydrogenase
KeywordsOXIDOREDUCTASE / alpha/beta fold / Rossmann-fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


zn-dependent alcohol dehydrogenase / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsKim, Y. / Marshall, N. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Zn-dependent Alcohol Dehydrogenases from Rhodobacter sphaeroides.
Authors: Kim, Y. / Marshall, N. / Keigher, L. / Joachimiak, A.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Zn-dependent Alcohol Dehydrogenase
B: Putative Zn-dependent Alcohol Dehydrogenase
C: Putative Zn-dependent Alcohol Dehydrogenase
D: Putative Zn-dependent Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,52612
Polymers117,7914
Non-polymers1,7368
Water4,540252
1
A: Putative Zn-dependent Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8462
Polymers29,4481
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative Zn-dependent Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9174
Polymers29,4481
Non-polymers4693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative Zn-dependent Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8462
Polymers29,4481
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative Zn-dependent Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9174
Polymers29,4481
Non-polymers4693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.883, 179.883, 83.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Putative Zn-dependent Alcohol Dehydrogenase


Mass: 29447.717 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: RHOS4_40580, RSP_4162 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q3IV08
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 25 % w/v PEG 3550, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→48.77 Å / Num. all: 38199 / Num. obs: 38199 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 40.05 Å2 / Rsym value: 0.13 / Net I/σ(I): 6.3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1878 / Rsym value: 0.659 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.4_147)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.769 Å / SU ML: 0.38 / Isotropic thermal model: mix / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1906 5.02 %random
Rwork0.176 ---
all0.179 37950 --
obs0.179 37950 99.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7388 Å20 Å2-0 Å2
2--4.7388 Å20 Å2
3----9.4775 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8056 0 112 252 8420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148371
X-RAY DIFFRACTIONf_angle_d1.46811341
X-RAY DIFFRACTIONf_dihedral_angle_d18.9183089
X-RAY DIFFRACTIONf_chiral_restr0.0931282
X-RAY DIFFRACTIONf_plane_restr0.0071471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.7-2.76750.32341170.227425602677100
2.7675-2.84240.29921390.226825362675100
2.8424-2.9260.28911410.228925622703100
2.926-3.02040.29121400.222925482688100
3.0204-3.12840.26891440.211725412685100
3.1284-3.25360.31481390.197625812720100
3.2536-3.40160.22591350.180825672712100
3.4016-3.58090.24811490.17825522711100
3.5809-3.80520.24131200.159326182738100
3.8052-4.09890.20081370.154125832720100
4.0989-4.51110.20541460.129725912737100
4.5111-5.16320.17111410.11982593273499
5.1632-6.50270.21361310.15362610274198
6.5027-48.77670.19211270.15152602272992
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.47740.1554-0.00820.56150.35850.45570.0689-0.0496-0.00550.0139-0.1067-0.04830.0002-0.08390.03330.07630.00390.0080.1080.01890.092316.740749.826933.9633
20.4105-0.0282-0.2662-0.0895-0.00591.8174-0.03820.0415-0.0530.1065-0.0506-0.0185-0.41-0.19210.0820.19770.0509-0.01350.05280.01680.083
30.2977-0.06940.0980.1203-0.02050.60060.0012-0.0159-0.022-0.0682-0.0502-0.0009-0.057300.03690.13280.0007-0.0160.0770.00090.1175
40.0746-0.29980.20250.6871-0.27580.6584-0.0589-0.03480.02-0.01540.0653-0.0516-0.0087-0.06920.00230.04320.02450.01840.07290.01880.0946
Refinement TLS groupSelection details: chain D

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