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- PDB-3ip1: Structure of putative alcohol dehydrogenase (TM_042) from Thermot... -

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Basic information

Entry
Database: PDB / ID: 3ip1
TitleStructure of putative alcohol dehydrogenase (TM_042) from Thermotoga maritima
ComponentsAlcohol dehydrogenase, zinc-containing
KeywordsOXIDOREDUCTASE / structural genomics / alcohol dehydrogenase / Metal-binding / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


inositol metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / zinc ion binding
Similarity search - Function
: / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal ...: / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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
: / Scyllo-inosose 3-dehydrogenase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of putative alcohol dehydrogenase (TM_042) from Thermotoga maritima
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionAug 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Alcohol dehydrogenase, zinc-containing
B: Alcohol dehydrogenase, zinc-containing
C: Alcohol dehydrogenase, zinc-containing
D: Alcohol dehydrogenase, zinc-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,46217
Polymers179,3294
Non-polymers1,13313
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-99 kcal/mol
Surface area55460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.365, 131.555, 161.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Alcohol dehydrogenase, zinc-containing


Mass: 44832.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0412, TM_0422 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYP3
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE AUTHORS STATE THAT THE IDENTITY OF HEAVY ATOM IS UNKNOWN. ASSIGNMENT 'CD' IS PURELY BASED ON ...THE AUTHORS STATE THAT THE IDENTITY OF HEAVY ATOM IS UNKNOWN. ASSIGNMENT 'CD' IS PURELY BASED ON DENSITY AND ITS INTERACTIONS WITH NEIGHBORING RESIDUES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, 0.2M MgCl2, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9793
SYNCHROTRONAPS 24-ID-E20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 25, 2009
ADSC QUANTUM 3152CCDNov 26, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21
ReflectionResolution: 2.09→50 Å / Num. obs: 94344 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.125 / Χ2: 1.586 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.1660.839196941.1681,299.8
2.16-2.255.80.635197303.2341,299.8
2.25-2.355.9197262.1061,299.8
2.35-2.486.30.4197711.1081,299.9
2.48-2.636.30.297197861.1581,2100
2.63-2.846.40.202197251.2391,2100
2.84-3.126.50.144197561.3821,2100
3.12-3.576.60.102197661.5041,2100
3.57-4.56.20.081197001.7331,299.7
4.5-506.50.068197841.4431,299.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.815 / SU B: 5.151 / SU ML: 0.135 / SU R Cruickshank DPI: 0.262 / SU Rfree: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4708 5 %RANDOM
Rwork0.207 ---
all0.209 ---
obs0.209 94344 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.83 Å2 / Biso mean: 32.189 Å2 / Biso min: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20 Å2
2--1.83 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.09→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12177 0 18 610 12805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212482
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.96816941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00951589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11523.764526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.594152119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8921590
X-RAY DIFFRACTIONr_chiral_restr0.0840.21895
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219430
X-RAY DIFFRACTIONr_mcbond_it0.5911.57865
X-RAY DIFFRACTIONr_mcangle_it1.115212695
X-RAY DIFFRACTIONr_scbond_it1.91234617
X-RAY DIFFRACTIONr_scangle_it3.2714.54242
LS refinement shellResolution: 2.09→2.146 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 340 -
Rwork0.216 6975 -
all-7315 -
obs--97.49 %

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