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- PDB-3gqj: Crystal structure of Cell Inhibiting Factor (Cif) from Photorhabd... -

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Basic information

Entry
Database: PDB / ID: 3gqj
TitleCrystal structure of Cell Inhibiting Factor (Cif) from Photorhabdus luminescens
ComponentsCell Inhibiting Factor (Cif)
KeywordsUNKNOWN FUNCTION / CIF / cell inhibiting factor / protease-like
Function / homologyProtein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / protein-glutamine glutaminase / symbiont-mediated perturbation of host cell cycle progression / toxin activity / hydrolase activity / host cell nucleus / extracellular region / Protein-glutamine deamidase Cif
Function and homology information
Biological speciesPhotorhabdus luminescens subsp. laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Author supporting evidence
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET 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 (Cif)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9344
Polymers29,6531
Non-polymers2803
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cell Inhibiting Factor (Cif)
hetero molecules

A: Cell Inhibiting Factor (Cif)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8678
Polymers59,3072
Non-polymers5616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3090 Å2
ΔGint-40 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.130, 59.130, 293.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe authors gel filtration experiments suggest the protein is a mixture of monomer and dimer in solution

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Components

#1: Protein Cell Inhibiting Factor (Cif)


Mass: 29653.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (bacteria)
Gene: plu2515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N439
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100 mM tri-Sodium Citrate pH 6.2, 2.45 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.85→41.96 Å / Num. all: 26540 / Num. obs: 26540 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12 % / Rsym value: 0.095 / Net I/σ(I): 19.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.387 / % possible all: 88.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MLPHAREphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→38.58 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 1338 5.1 %RANDOM
Rwork0.22585 ---
obs0.22819 25084 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20.63 Å20 Å2
2--1.26 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 17 198 2190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222078
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9762823
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3375265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36226.132106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82715386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1411510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211574
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_it0.7181.51266
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3222059
X-RAY DIFFRACTIONr_scbond_it2.0483812
X-RAY DIFFRACTIONr_scangle_it3.5624.5757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 81 -
Rwork0.27 1555 -
obs--84.29 %

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