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- PDB-3efy: Structure of the Cyclomodulin Cif from Pathogenic Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3efy
TitleStructure of the Cyclomodulin Cif from Pathogenic Escherichia coli
ComponentsCif (Cell cycle inhibiting factor)
KeywordsCELL CYCLE / Cif / bacteria / virulence factor / type III secretion / E. coli / Plasmid
Function / homologyProtein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / cell division / Cell division protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsStebbins, C.E. / Hsu, Y.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the cyclomodulin Cif from pathogenic Escherichia coli.
Authors: Hsu, Y. / Jubelin, G. / Taieb, F. / Nougayrede, J.P. / Oswald, E. / Stebbins, C.E.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cif (Cell cycle inhibiting factor)
B: Cif (Cell cycle inhibiting factor)


Theoretical massNumber of molelcules
Total (without water)44,8812
Polymers44,8812
Non-polymers00
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-37 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.768, 111.768, 107.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

21A-532-

HOH

31B-450-

HOH

41B-504-

HOH

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Components

#1: Protein Cif (Cell cycle inhibiting factor)


Mass: 22440.434 Da / Num. of mol.: 2 / Fragment: UNP residues 100-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cif / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WRZ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 1.85M Sodium Malonate, 0.1M tri-sodium citrate dihydrate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 74589

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→45.33 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.555 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22202 3755 5 %RANDOM
Rwork0.18056 ---
obs0.18262 70675 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 0 751 3667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222969
X-RAY DIFFRACTIONr_bond_other_d0.0010.022021
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.963999
X-RAY DIFFRACTIONr_angle_other_deg0.95234944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08125.563151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09615543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7751512
X-RAY DIFFRACTIONr_chiral_restr0.10.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
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_refined0.2450.2637
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1741.51815
X-RAY DIFFRACTIONr_mcbond_other0.3121.5742
X-RAY DIFFRACTIONr_mcangle_it2.23922920
X-RAY DIFFRACTIONr_scbond_it3.331154
X-RAY DIFFRACTIONr_scangle_it5.2794.51079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 264 -
Rwork0.25 5219 -
obs--99.69 %

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