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- PDB-1o89: Crystal structure of E. COLI K-12 yhdH -

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Basic information

Entry
Database: PDB / ID: 1o89
TitleCrystal structure of E. COLI K-12 yhdH
ComponentsYHDH
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / POSSIBLE NADPH-DEPENDENT QUINONE OXIDOREDUCTASE
Function / homology
Function and homology information


acrylyl-CoA reductase (NADPH) / acryloyl-CoA reductase (NADPH) activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Acrylyl-CoA reductase AcuI / 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 ...Acrylyl-CoA reductase AcuI / 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
Probable acrylyl-CoA reductase AcuI
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsSulzenbacher, G. / Roig-Zamboni, V. / Pagot, F. / Grisel, S. / Salamoni, A. / Valencia, C. / Bignon, C. / Vincentelli, R. / Tegoni, M. / Cambillau, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the Escherichia Coli Yhdh, a Putative Quinone Oxidoreductase
Authors: Sulzenbacher, G. / Roig-Zamboni, V. / Pagot, F. / Grisel, S. / Salamoni, A. / Valencia, C. / Campanacci, V. / Vincentelli, R. / Tegoni, M. / Eklund, H. / Cambillau, C.
History
DepositionNov 26, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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: YHDH


Theoretical massNumber of molelcules
Total (without water)37,2941
Polymers37,2941
Non-polymers00
Water93752
1
A: YHDH

A: YHDH


Theoretical massNumber of molelcules
Total (without water)74,5892
Polymers74,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
MethodPQS
Unit cell
Length a, b, c (Å)55.671, 55.671, 201.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein YHDH / B3253 / YHDH


Mass: 37294.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P26646
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENTRY IS FROM A STRUCTURAL GENOMICS EXPERIMENT, POSSIBLY A NADPH-DEPENDENT QUINONE OXIDOREDUCTASE
Sequence detailsRESIDUES -20 TO 0 AND 10 TO 12 MISSING FROM DECK OF COORDINATES. RESIDUES -20 TO 0 ARE FROM THE ...RESIDUES -20 TO 0 AND 10 TO 12 MISSING FROM DECK OF COORDINATES. RESIDUES -20 TO 0 ARE FROM THE EXPRESSION TAG AT THE N-TERMINUS

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: 39 % PEG 600, 0.1 M HEPES PH 7.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
139 %PEG6001drop
20.1 %(w/v)satHEPES1droppH7.5
36 mg/mlprotein1drop
45 mMNADP1drop
50.1 mM1dropZnCl2
68.5 %PEG80001reservoir
70.1 Msodium acetate1reservoirpH5.5
80.01 mM1reservoirZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→19.7 Å / Num. obs: 15661 / % possible obs: 99.1 % / Redundancy: 8.6 % / Biso Wilson estimate: 50.08 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.7
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 20 Å / Num. obs: 15944 / Redundancy: 8.6 % / Num. measured all: 426724 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 99.7 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: YHDH DETERMINED BY MAD

Resolution: 2.25→12 Å / SU B: 6.426 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23669 1550 9.9 %RANDOM
Rwork0.19703 ---
obs0.20087 14074 99.01 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.25→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 0 52 2458
Refinement
*PLUS
Lowest resolution: 12 Å / Rfactor Rfree: 0.2367 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.011
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.16

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