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- PDB-3gqm: Crystal structure of Cell Inhibiting Factor (Cif) from Burkholder... -

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Basic information

Entry
Database: PDB / ID: 3gqm
TitleCrystal structure of Cell Inhibiting Factor (Cif) from Burkholderia pseudomallei (CifBp)
ComponentsCell Inhibiting Factor (CifBp)
KeywordsUNKNOWN FUNCTION / Cell Inhibiting factor / Cif / CifBp
Function / homology
Function and homology information


protein-glutamine glutaminase activity / protein-glutamine glutaminase / symbiont-mediated perturbation of host cell cycle progression / toxin activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell nucleus / extracellular region
Similarity search - Function
Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF)
Similarity search - Domain/homology
Protein-glutamine deamidase Cif
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCrow, A. / Banfield, M.J.
CitationJournal: Plos One / Year: 2009
Title: Crystal structures of Cif from bacterial pathogens Photorhabdus luminescens and Burkholderia pseudomallei.
Authors: Crow, A. / Race, P.R. / Jubelin, G. / Varela Chavez, C. / Escoubas, J.M. / Oswald, E. / Banfield, M.J.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell Inhibiting Factor (CifBp)
B: Cell Inhibiting Factor (CifBp)


Theoretical massNumber of molelcules
Total (without water)61,7082
Polymers61,7082
Non-polymers00
Water1,65792
1
A: Cell Inhibiting Factor (CifBp)


Theoretical massNumber of molelcules
Total (without water)30,8541
Polymers30,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell Inhibiting Factor (CifBp)


Theoretical massNumber of molelcules
Total (without water)30,8541
Polymers30,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.893, 77.744, 115.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell Inhibiting Factor (CifBp)


Mass: 30854.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BPSS1385 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63KH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.89 Å3/Da / Density % sol: 35.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 % (w/v) PEG 8000, 100 mM HEPES 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.92 Å
DetectorDetector: CCD / Date: Jun 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→22.01 Å / Num. all: 29440 / Num. obs: 29440 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rsym value: 0.05 / Net I/σ(I): 20.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.374 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0061refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GQJ

3gqj


Resolution: 2.1→22.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25883 1493 5.1 %RANDOM
Rwork0.20881 ---
obs0.21138 27890 99.78 %-
all-29440 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.052 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2--0.14 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→22.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 0 92 4017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223941
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9645346
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68624.262183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77715672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3691527
X-RAY DIFFRACTIONr_chiral_restr0.1110.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212987
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9531.52471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7723983
X-RAY DIFFRACTIONr_scbond_it2.85231470
X-RAY DIFFRACTIONr_scangle_it4.6534.51363
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 106 -
Rwork0.241 2022 -
obs--99.77 %

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