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- PDB-1uay: Crystal Structure of Type II 3-Hydroxyacyl-CoA Dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 1uay
TitleCrystal Structure of Type II 3-Hydroxyacyl-CoA Dehydrogenase from Thermus thermophilus HB8
ComponentsType II 3-hydroxyacyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / BETA OXIDATION / FATTY ACID / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / Oxidoreductase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKunishima, N. / Asada, Y. / Yokoyama, S. / Kuramitsu, S. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Type II 3-Hydroxyacyl-CoA Dehydrogenase from Thermus thermophilus HB8
Authors: Kunishima, N. / Asada, Y. / Yokoyama, S. / Kuramitsu, S. / Miyano, M.
History
DepositionMar 25, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Type II 3-hydroxyacyl-CoA dehydrogenase
B: Type II 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7904
Polymers51,2552
Non-polymers5342
Water10,521584
1
A: Type II 3-hydroxyacyl-CoA dehydrogenase
B: Type II 3-hydroxyacyl-CoA dehydrogenase
hetero molecules

A: Type II 3-hydroxyacyl-CoA dehydrogenase
B: Type II 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5798
Polymers102,5104
Non-polymers1,0694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area16840 Å2
ΔGint-102 kcal/mol
Surface area31230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.930, 94.871, 113.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1200-

HOH

DetailsThe biological assembly is tetramer generated from the dimer in the asymmetric unit by the operation: -x+1,y,-z+1/2

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Components

#1: Protein Type II 3-hydroxyacyl-CoA dehydrogenase


Mass: 25627.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIA1
#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

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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: 1.79 Å3/Da / Density % sol: 30.69 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.7
Details: sodium phosphate, pH 4.7, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 3, 2002 / Details: mirrors
RadiationMonochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 83399 / Num. obs: 83399 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.092 / Net I/σ(I): 7.7
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.81 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.9 / Num. unique all: 8288 / Rsym value: 0.697 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E6W

1e6w


Resolution: 1.4→29.6 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4144 -RANDOM
Rwork0.181 ---
all0.182 83103 --
obs0.182 83103 99.2 %-
Displacement parametersBiso mean: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2--1.54 Å20 Å2
3----2.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3571 0 38 584 4193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.0051
LS refinement shellResolution: 1.4→1.46 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.233 511 -
Rwork0.214 --
obs-9838 100 %

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