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- PDB-1uuf: crystal structure of a zinc-type alcohol dehydrogenase-like prote... -

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Basic information

Entry
Database: PDB / ID: 1uuf
Titlecrystal structure of a zinc-type alcohol dehydrogenase-like protein yahK
ComponentsZINC-TYPE ALCOHOL DEHYDROGENASE-LIKE PROTEIN YAHK
KeywordsOXIDOREDUCTASE / ZINC BINDING / OXYDOREDUCTASE / METAL-BINDING / BACTERIAL TARGETS AT IGS-CNRS / FRANCE / BIGS / STRUCTURAL GENOMICS
Function / homology
Function and homology information


alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / zinc ion binding
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 ...: / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
Aldehyde reductase YahK
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
AuthorsJeudy, S. / Claverie, J.M. / Abergel, C.
CitationJournal: To be Published
Title: Crystal Structure of a Yahk, a Zinc-Type Alcohol Dehydrogenase-Like Protein
Authors: Jeudy, S. / Claverie, J.M. / Abergel, C.
History
DepositionDec 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZINC-TYPE ALCOHOL DEHYDROGENASE-LIKE PROTEIN YAHK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5643
Polymers40,4331
Non-polymers1312
Water6,756375
1
A: ZINC-TYPE ALCOHOL DEHYDROGENASE-LIKE PROTEIN YAHK
hetero molecules

A: ZINC-TYPE ALCOHOL DEHYDROGENASE-LIKE PROTEIN YAHK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1286
Polymers80,8662
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)69.536, 78.805, 70.685
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2182-

HOH

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Components

#1: Protein ZINC-TYPE ALCOHOL DEHYDROGENASE-LIKE PROTEIN YAHK / YAHK


Mass: 40432.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THERE ARE TWO ZINC BINDING TO THE MOLECULE 7 RESIDUES (270-276) ARE MISSING IN THE STRUCTURE
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P75691
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE ZINC-CONTAINING ALCOHOL DEHYDROGENASE FAMILY. HIGHLY SIMILAR TO PLANTS CINNAMYL- ...BELONGS TO THE ZINC-CONTAINING ALCOHOL DEHYDROGENASE FAMILY. HIGHLY SIMILAR TO PLANTS CINNAMYL-ALCOHOL DEHYDROGENASES.

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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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growpH: 4.75
Details: 14% MPD, NACL 0.1M, TRIS 0.1M, SODIUM ACETATE 10MM, ZN ACETATE 0.1MM, PH 4.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.2839,1.846,0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2003 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28391
21.8461
30.97961
ReflectionResolution: 1.76→1.86 Å / Num. obs: 35671 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 5.6
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.76→19.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 278526.54 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1755 4.9 %RANDOM
Rwork0.184 ---
obs0.184 35478 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2388 Å2 / ksol: 0.368296 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å2-0.08 Å2
2--0.01 Å20 Å2
3----1.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.76→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 2 375 2960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 1.76→1.87 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 287 4.9 %
Rwork0.255 5559 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAION.TO
X-RAY DIFFRACTION4CISPEP.PARAM

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