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- PDB-2qwu: Crystal structure of F. tularensis pathogenicity island protein C -

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Basic information

Entry
Database: PDB / ID: 2qwu
TitleCrystal structure of F. tularensis pathogenicity island protein C
ComponentsIntracellular growth locus, subunit C
KeywordsCELL INVASION / Francisella tularensis / iglc
Function / homologyIntracellular growth locus C protein / Intracellular growth locus C protein / Intracellular growth locus, subunit C
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsSun, P. / Austin, B.P. / Schubot, F.D. / Waugh, D.S.
CitationJournal: To be Published
Title: Crystal structure of Francisella tularensis pathogenicity island protein IglC
Authors: Sun, P. / Austin, B.P. / Schubot, F.D. / Waugh, D.S.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intracellular growth locus, subunit C
B: Intracellular growth locus, subunit C


Theoretical massNumber of molelcules
Total (without water)45,8302
Polymers45,8302
Non-polymers00
Water7,746430
1
A: Intracellular growth locus, subunit C


Theoretical massNumber of molelcules
Total (without water)22,9151
Polymers22,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intracellular growth locus, subunit C


Theoretical massNumber of molelcules
Total (without water)22,9151
Polymers22,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.031, 83.991, 89.838
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 Intracellular growth locus, subunit C


Mass: 22914.965 Da / Num. of mol.: 2 / Mutation: L36M, L76M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Species: Francisella tularensis / Strain: subsp. tularensis / Gene: iglC2, iglC1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5NEC5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.05 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl pH 8.5, 27-30% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2007 / Details: mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.65→35 Å / Num. obs: 78172 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3467 / % possible all: 78.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SGXPROmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→35 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: anomalous data set was used in refinement. THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3799 -random
Rwork0.184 ---
obs0.184 78172 90.7 %-
Displacement parametersBiso mean: 27.2532 Å2
Baniso -1Baniso -2Baniso -3
1--8.96 Å20 Å20 Å2
2--4.203 Å20 Å2
3---4.757 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.65→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 0 430 3534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.404
X-RAY DIFFRACTIONc_mcangle_it2.112
LS refinement shellResolution: 1.65→1.71 Å
RfactorNum. reflection% reflection
Rfree0.3365 236 -
Rwork0.2736 --
obs-4638 95.2 %

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