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- PDB-2qm0: Crystal structure of BES protein from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 2qm0
TitleCrystal structure of BES protein from Bacillus cereus
ComponentsBES
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta structure / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / IroE protein
Function and homology information
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.84 Å
AuthorsKim, Y. / Maltseva, N. / Zawadzka, A. / Holzle, D. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of BES from Bacillus cereus.
Authors: Kim, Y. / Maltseva, N. / Zawadzka, A. / Holzle, D. / Joachimiak, A.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Remark 300 BIOMOLECULE: 1 AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. SEE REMARK 350 ... BIOMOLECULE: 1 AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA.
Remark 600 HETEROGEN DIISOPROPYLPHOSPHONO GROUP IS COVALENTLY BOUND TO SERINE 157

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BES
B: BES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1307
Polymers62,6502
Non-polymers4805
Water9,692538
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570/22760
MethodPISA
2
A: BES
B: BES
hetero molecules

A: BES
B: BES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,26014
Polymers125,2994
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area13210/43450
MethodPISA
Unit cell
Length a, b, c (Å)48.849, 135.058, 200.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-831-

HOH

21A-840-

HOH

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Components

#1: Protein BES


Mass: 31324.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: DSM 31 / Gene: BC_3734 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81A57
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6.5, 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97930, 0.97950
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2007 / Details: mirrors
RadiationMonochromator: double crystal, Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
ReflectionResolution: 1.84→45.94 Å / Num. all: 55348 / Num. obs: 55348 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rsym value: 0.099 / Net I/σ(I): 10.1
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 4.3 % / Num. unique all: 3752 / Rsym value: 0.499 / % possible all: 65.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
CCP4phasing
ARP/wARPmodel building
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.84→45.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.882 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.14
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.22828 5567 10.1 %RANDOM
Rwork0.18444 ---
all0.18879 49733 --
obs0.18879 49733 95.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---1.59 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 25 538 4828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224576
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.9586211
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.80625.07213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.115799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5211512
X-RAY DIFFRACTIONr_chiral_restr0.2680.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023472
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22330
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23095
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2461
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9361.52838
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47824445
X-RAY DIFFRACTIONr_scbond_it2.35832009
X-RAY DIFFRACTIONr_scangle_it3.6024.51766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 245 -
Rwork0.311 2334 -
obs-2579 60.71 %

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