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- PDB-3eir: Crystal structure of CHBP, a Cif Homologue from Burkholderia pseu... -

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Basic information

Entry
Database: PDB / ID: 3eir
TitleCrystal structure of CHBP, a Cif Homologue from Burkholderia pseudomallei
ComponentsPutative ATP/GTP binding protein
KeywordsUNKNOWN FUNCTION / papain-like fold
Function / homologyProtein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase activity / protein-glutamine glutaminase / toxin activity / host cell nucleus / extracellular region / Protein-glutamine deamidase Cif
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.101 Å
AuthorsYao, Q. / Zhu, Y. / Shao, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle
Authors: Yao, Q. / Cui, J. / Zhu, Y. / Wang, G. / Hu, L. / Long, C. / Cao, R. / Liu, X. / Huang, N. / Chen, S. / Liu, L. / Shao, F.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ATP/GTP binding protein
B: Putative ATP/GTP binding protein


Theoretical massNumber of molelcules
Total (without water)62,6172
Polymers62,6172
Non-polymers00
Water4,558253
1
A: Putative ATP/GTP binding protein


Theoretical massNumber of molelcules
Total (without water)31,3081
Polymers31,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ATP/GTP binding protein


Theoretical massNumber of molelcules
Total (without water)31,3081
Polymers31,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.783, 79.916, 117.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative ATP/GTP binding protein / the EPEC effector Cif Homologue


Mass: 31308.439 Da / Num. of mol.: 2 / Fragment: residues 48-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: YP_111397 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q63KH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 30780 / Num. obs: 30618 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2990 / Rsym value: 0.318 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementResolution: 2.101→33.033 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.737 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3075 10.06 %RANDOM
Rwork0.193 ---
obs0.199 30558 99.35 %-
all-30758 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.007 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 161.73 Å2 / Biso mean: 58.918 Å2 / Biso min: 26.73 Å2
Baniso -1Baniso -2Baniso -3
1-21.291 Å2-0 Å2-0 Å2
2---8.547 Å20 Å2
3----12.744 Å2
Refinement stepCycle: LAST / Resolution: 2.101→33.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 0 253 4121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063937
X-RAY DIFFRACTIONf_angle_d0.9475331
X-RAY DIFFRACTIONf_chiral_restr0.065605
X-RAY DIFFRACTIONf_plane_restr0.004692
X-RAY DIFFRACTIONf_dihedral_angle_d15.8731453
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.101-2.1340.371210.2631149127094
2.134-2.1690.2741200.24112611381100
2.169-2.2070.321400.2312421382100
2.207-2.2470.321540.23711931347100
2.247-2.290.3761380.23712691407100
2.29-2.3360.3241480.24312111359100
2.336-2.3870.3121540.22712421396100
2.387-2.4430.3231350.2212281363100
2.443-2.5040.3461140.23412881402100
2.504-2.5720.2831330.22912311364100
2.572-2.6470.2871420.22612441386100
2.647-2.7330.3271500.22612571407100
2.733-2.830.2861610.22412161377100
2.83-2.9440.3021400.21912551395100
2.944-3.0770.2881350.2312551390100
3.077-3.240.2841330.21212751408100
3.24-3.4420.2331310.20512651396100
3.442-3.7080.2491530.18512531406100
3.708-4.080.2461310.16112731404100
4.08-4.6690.1891470.13912921439100
4.669-5.8770.1851500.1513001450100
5.877-33.0370.2241450.1741284142993
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.9746-1.09680.25820.6517-0.07910.5956-0.0697-0.2378-0.26060.39720.16470.1750.3799-0.1376-0.00030.3861-0.06750.10830.39650.0120.4516(chain A and resid 31:104)32.342837.897559.528
22.192-0.5540.87843.9502-0.04553.33960.08720.2857-0.0907-0.09220.0468-0.180.73150.734200.41490.15980.05210.4603-0.02670.2989(chain A and resid 105:280)52.203232.223255.6745
31.3251-0.81431.26571.21171.19191.50450.29930.1465-0.1476-0.7021-0.3475-0.06960.4212-0.19370.04240.6920.05610.13630.3287-0.01270.3631(chain B and resid 32:104)35.554536.1434.7883
42.5265-1.6862-0.25964.17851.38332.0074-0.0431-0.11840.2078-0.3373-0.0679-0.28420.08530.20720.00010.40180.03690.13280.37420.04840.3815(chain B and resid 105:280)37.234156.822340.5521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 31:104)A31 - 104
2X-RAY DIFFRACTION2(chain A and resid 105:280)A105 - 280
3X-RAY DIFFRACTION3(chain B and resid 32:104)B32 - 104
4X-RAY DIFFRACTION4(chain B and resid 105:280)B105 - 280

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