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- PDB-3nwz: Crystal Structure of BH2602 protein from Bacillus halodurans with... -

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Basic information

Entry
Database: PDB / ID: 3nwz
TitleCrystal Structure of BH2602 protein from Bacillus halodurans with CoA, Northeast Structural Genomics Consortium Target BhR199
ComponentsBH2602 protein
KeywordsStructural Genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


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
COENZYME A / BH2602 protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.566 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target BhR199
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH2602 protein
B: BH2602 protein
C: BH2602 protein
D: BH2602 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4357
Polymers80,4754
Non-polymers9603
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-83 kcal/mol
Surface area26000 Å2
MethodPISA
2
A: BH2602 protein
C: BH2602 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1014
Polymers40,2372
Non-polymers8642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-39 kcal/mol
Surface area15640 Å2
MethodPISA
3
B: BH2602 protein
D: BH2602 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3343
Polymers40,2372
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-36 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.243, 89.733, 71.850
Angle α, β, γ (deg.)90.00, 107.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BH2602 protein


Mass: 20118.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH2602 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9K9P3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.2M ammonium sulfate, 0.1M hepes, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2010 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 38995 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 48.09 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.566→27.883 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 31.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1022 5.1 %
Rwork0.2309 --
obs0.2326 20053 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.564 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.2745 Å20 Å2-22.7357 Å2
2---20.9524 Å2-0 Å2
3---12.6778 Å2
Refinement stepCycle: LAST / Resolution: 2.566→27.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4607 0 58 16 4681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094725
X-RAY DIFFRACTIONf_angle_d1.3316392
X-RAY DIFFRACTIONf_dihedral_angle_d19.4991806
X-RAY DIFFRACTIONf_chiral_restr0.097743
X-RAY DIFFRACTIONf_plane_restr0.007823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5662-2.70140.39811280.3042517X-RAY DIFFRACTION91
2.7014-2.87050.3621460.27442753X-RAY DIFFRACTION100
2.8705-3.09180.30691640.26822694X-RAY DIFFRACTION100
3.0918-3.40250.31771420.2432751X-RAY DIFFRACTION100
3.4025-3.89370.25661390.21952767X-RAY DIFFRACTION100
3.8937-4.90130.20341370.17622770X-RAY DIFFRACTION100
4.9013-27.88430.20581660.21832779X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 28.2716 Å / Origin y: 34.0439 Å / Origin z: 33.6898 Å
111213212223313233
T0.0734 Å2-0.0042 Å2-0.0125 Å2-0.1122 Å20.0106 Å2--0.1518 Å2
L0.0029 °2-0.4697 °20.0076 °2-0.9665 °20.1733 °2--0.5417 °2
S0.0442 Å °0.0031 Å °-0.0888 Å °-0.0927 Å °-0.062 Å °0.3107 Å °-0.0117 Å °0.0198 Å °0.0018 Å °
Refinement TLS groupSelection details: all

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