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

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Basic information

Entry
Database: PDB / ID: 2egr
TitleCrystal Structure of Hypothetical Protein(AQ1494) from Aquifex aeolicus
ComponentsHypothetical protein aq_1494Hypothesis
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 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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
Water2,918162
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 operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)102.482, 102.482, 53.067
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Hypothetical protein aq_1494 / Hypothesis


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 / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 293 K / Method: oil batch / pH: 8.5
Details: 0.1M Tris-HCl pH8.5, 2M Ammonium Sulfate, 15% Glycerol, oil batch, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 17, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 29594 / Num. obs: 29594 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.373 / Num. unique all: 2917 / % possible all: 99.8

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Processing

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

2egi


Resolution: 1.8→45.55 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.635 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24455 1499 5.1 %RANDOM
Rwork0.21993 ---
obs0.22121 28057 99.61 %-
all-29594 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 162 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222176
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9482924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6025250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3922.807114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84815392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.761516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021656
X-RAY DIFFRACTIONr_nbd_refined0.2110.2938
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.220
X-RAY DIFFRACTIONr_mcbond_it1.1421.51301
X-RAY DIFFRACTIONr_mcangle_it1.59822028
X-RAY DIFFRACTIONr_scbond_it2.75631012
X-RAY DIFFRACTIONr_scangle_it3.9424.5896
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 115 -
Rwork0.242 2034 -
obs--99.77 %

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