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- PDB-2egj: Crystal Structure of Hypothetical Protein(AQ1494) from Aquifex ae... -

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Basic information

Entry
Database: PDB / ID: 2egj
TitleCrystal Structure of Hypothetical Protein(AQ1494) from Aquifex aeolicus
ComponentsHypothetical protein aq_1494
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical Protein / Aquifex aeolicus / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity / Hydrolases; Acting on ester bonds
Similarity search - Function
4-hydroxybenzoyl-CoA thioesterase, active site / 4-hydroxybenzoyl-CoA thioesterase family active site. / Acyl-CoA thioester hydrolase YbgC/YbaW family / Thioesterase-like superfamily / : / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Putative esterase aq_1494
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumarevel, T.S. / Niwa, H. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical Protein(AQ1494) from Aquifex aeolicus
Authors: Kumarevel, T.S. / Niwa, H. / Kuramitsu, S. / Yokoyama, S.
History
DepositionMar 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein aq_1494
B: Hypothetical protein aq_1494


Theoretical massNumber of molelcules
Total (without water)30,6172
Polymers30,6172
Non-polymers00
Water2,720151
1
A: Hypothetical protein aq_1494
B: Hypothetical protein aq_1494

A: Hypothetical protein aq_1494
B: Hypothetical protein aq_1494


Theoretical massNumber of molelcules
Total (without water)61,2354
Polymers61,2354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8470 Å2
ΔGint-22 kcal/mol
Surface area21600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.468, 69.426, 84.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hypothetical protein aq_1494


Mass: 15308.683 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: AQ1494 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL-X / References: UniProt: O67466
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M Sodium chloride, 0.1M Phosphate-citrate, 50% PEG200, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97943 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 16, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 29686 / Num. obs: 29686 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.279 / Num. unique all: 2929 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EGI

2egi


Resolution: 1.8→45.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.042 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22062 1502 5.1 %RANDOM
Rwork0.19716 ---
obs0.19838 28150 99.93 %-
all-29686 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.72 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 151 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222176
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9482924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01222.807114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02715392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9941516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021656
X-RAY DIFFRACTIONr_nbd_refined0.2120.2895
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21505
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.217
X-RAY DIFFRACTIONr_mcbond_it11.51297
X-RAY DIFFRACTIONr_mcangle_it1.50622028
X-RAY DIFFRACTIONr_scbond_it2.61531007
X-RAY DIFFRACTIONr_scangle_it3.944.5896
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 95 -
Rwork0.223 2070 -
obs--99.82 %

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