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- PDB-1uls: Crystal structure of tt0140 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1uls
TitleCrystal structure of tt0140 from Thermus thermophilus HB8
Componentsputative 3-oxoacyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / reductase / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
3-oxoacyl-[acyl carrier protein] reductase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHisanaga, Y. / Ago, H. / Hamada, K. / Sugahara, M. / Nodake, Y. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of tt0140 from Thermus thermophilus HB8
Authors: Hisanaga, Y. / Ago, H. / Hamada, K. / Sugahara, M. / Nodake, Y. / Kuramitsu, S. / Yokoyama, S. / Miyano, M.
History
DepositionSep 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative 3-oxoacyl-acyl carrier protein reductase
B: putative 3-oxoacyl-acyl carrier protein reductase
C: putative 3-oxoacyl-acyl carrier protein reductase
D: putative 3-oxoacyl-acyl carrier protein reductase
E: putative 3-oxoacyl-acyl carrier protein reductase
F: putative 3-oxoacyl-acyl carrier protein reductase
G: putative 3-oxoacyl-acyl carrier protein reductase
H: putative 3-oxoacyl-acyl carrier protein reductase


Theoretical massNumber of molelcules
Total (without water)210,2598
Polymers210,2598
Non-polymers00
Water12,665703
1
A: putative 3-oxoacyl-acyl carrier protein reductase
B: putative 3-oxoacyl-acyl carrier protein reductase
C: putative 3-oxoacyl-acyl carrier protein reductase
D: putative 3-oxoacyl-acyl carrier protein reductase


Theoretical massNumber of molelcules
Total (without water)105,1304
Polymers105,1304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13670 Å2
ΔGint-103 kcal/mol
Surface area33090 Å2
MethodPISA
2
E: putative 3-oxoacyl-acyl carrier protein reductase
F: putative 3-oxoacyl-acyl carrier protein reductase
G: putative 3-oxoacyl-acyl carrier protein reductase
H: putative 3-oxoacyl-acyl carrier protein reductase


Theoretical massNumber of molelcules
Total (without water)105,1304
Polymers105,1304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-103 kcal/mol
Surface area33680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.260, 77.330, 78.670
Angle α, β, γ (deg.)90.12, 90.96, 95.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
putative 3-oxoacyl-acyl carrier protein reductase


Mass: 26282.396 Da / Num. of mol.: 8 / Mutation: K152M/A175T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SK98, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.19 Å3/Da / Density % sol: 43.45 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 69802 / % possible obs: 98.2 %
Reflection shellResolution: 2.4→2.49 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.4 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 595437.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 6713 10.1 %RANDOM
Rwork0.196 ---
obs0.196 59713 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.054 Å2 / ksol: 0.286888 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20.8 Å2-5.3 Å2
2---8.05 Å2-0.16 Å2
3---10.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14541 0 0 703 15244
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.222.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 1002 9.9 %
Rwork0.249 9137 -
obs-9083 86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM

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