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- PDB-3dkz: Crystal structure of the Q7W9W5_BORPA protein from Bordetella par... -

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Basic information

Entry
Database: PDB / ID: 3dkz
TitleCrystal structure of the Q7W9W5_BORPA protein from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR208C.
ComponentsThioesterase superfamily protein
KeywordsHYDROLASE / Q7W9W5 / BORPA / thioesterase superfamily / PF03061 / NESG / BpR208C / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity
Similarity search - Function
Acyl-coenzyme A thioesterase 13 / Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Thioesterase domain-containing protein
Similarity search - Component
Biological speciesBordetella parapertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Q7W9W5_BORPA protein from Bordetella parapertussis.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Thioesterase superfamily protein
B: Thioesterase superfamily protein


Theoretical massNumber of molelcules
Total (without water)31,1642
Polymers31,1642
Non-polymers00
Water1,22568
1
A: Thioesterase superfamily protein
B: Thioesterase superfamily protein

A: Thioesterase superfamily protein
B: Thioesterase superfamily protein


Theoretical massNumber of molelcules
Total (without water)62,3284
Polymers62,3284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area7460 Å2
ΔGint-50 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.646, 69.646, 107.792
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thioesterase superfamily protein


Mass: 15581.942 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis (bacteria) / Strain: 12822/ATCC BAA-587/NCTC 13253 / Gene: BPP1634 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q7W9W5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 291 K / Method: microbatch-under-oil crystallization
Details: 26% PEG 4000, 0.17M ammonium sulfate, 15% glycerol, microbatch-under-oil crystallization , temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 45637 / Num. obs: 44952 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4595 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→35.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 720938.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1000 5 %RANDOM
Rwork0.238 ---
obs0.238 20030 87.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.7959 Å2 / ksol: 0.347748 e/Å3
Displacement parametersBiso mean: 59.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.13 Å26.9 Å20 Å2
2--5.13 Å20 Å2
3----10.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 68 1894
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 136 5.8 %
Rwork0.316 2213 -
obs--62 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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