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- PDB-4p40: Chlamydia pneumoniae CopN -

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Basic information

Entry
Database: PDB / ID: 4p40
TitleChlamydia pneumoniae CopN
ComponentsCopN
KeywordsTRANSPORT PROTEIN / TTSS / secretion system / Chlamydia / tubulin
Function / homology
Function and homology information


protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / cell surface
Similarity search - Function
Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain
Similarity search - Domain/homology
DIMETHYLAMINE / FORMYL GROUP / Low calcium response E
Similarity search - Component
Biological speciesChlamydia pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsNawrotek, A. / Guimaraes, B.G. / Knossow, M. / Gigant, B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Biochemical and Structural Insights into Microtubule Perturbation by CopN from Chlamydia pneumoniae.
Authors: Nawrotek, A. / Guimaraes, B.G. / Velours, C. / Subtil, A. / Knossow, M. / Gigant, B.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references / Structure summary
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CopN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,18113
Polymers46,6521
Non-polymers52912
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-44 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.796, 67.970, 85.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CopN / Low Calcium Response E / Low calcium response E / Type III secreted protein SctW


Mass: 46652.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia pneumoniae (bacteria) / Gene: lcrE, copN, CP_0433, CpB0334, CPn_0324 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE3 / References: UniProt: Q9Z8L4

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Non-polymers , 5 types, 461 molecules

#2: Chemical
ChemComp-FOR / FORMYL GROUP / Aldehyde


Mass: 30.026 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DMN / DIMETHYLAMINE / Dimethylamine


Mass: 45.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Lithium sulfate, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.2→41.563 Å / Num. obs: 118161 / % possible obs: 97 % / Redundancy: 3.53 % / Net I/σ(I): 10.72
Reflection shellResolution: 1.2→1.28 Å / Redundancy: 2 % / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata scaling
SHELXLrefinement
SCALAdata scaling
XSCALEdata scaling
BUSTER-TNTrefinement
RefinementResolution: 1.2→41.563 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 100 / Phase error: 16.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1624 5945 5.03 %
Rwork0.1433 --
obs0.1442 118128 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→41.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 27 449 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132397
X-RAY DIFFRACTIONf_angle_d1.4353275
X-RAY DIFFRACTIONf_dihedral_angle_d12.59907
X-RAY DIFFRACTIONf_chiral_restr0.087380
X-RAY DIFFRACTIONf_plane_restr0.008434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21360.33671700.33953357X-RAY DIFFRACTION88
1.2136-1.22790.32221880.30623404X-RAY DIFFRACTION91
1.2279-1.24290.30921720.28713462X-RAY DIFFRACTION91
1.2429-1.25860.27821960.25413546X-RAY DIFFRACTION92
1.2586-1.27520.23812080.21733539X-RAY DIFFRACTION95
1.2752-1.29270.23172050.20543672X-RAY DIFFRACTION97
1.2927-1.31110.21331850.18963747X-RAY DIFFRACTION98
1.3111-1.33070.21282050.18533697X-RAY DIFFRACTION97
1.3307-1.35150.19451940.17263726X-RAY DIFFRACTION98
1.3515-1.37370.20422080.17063754X-RAY DIFFRACTION98
1.3737-1.39730.18482140.16463725X-RAY DIFFRACTION98
1.3973-1.42270.18221990.16253744X-RAY DIFFRACTION98
1.4227-1.45010.1812270.14573746X-RAY DIFFRACTION99
1.4501-1.47970.16921860.12643744X-RAY DIFFRACTION98
1.4797-1.51190.14661930.11683779X-RAY DIFFRACTION98
1.5119-1.54710.14912010.113745X-RAY DIFFRACTION98
1.5471-1.58580.12952080.10543718X-RAY DIFFRACTION98
1.5858-1.62860.12651930.09843808X-RAY DIFFRACTION99
1.6286-1.67660.12452040.10493745X-RAY DIFFRACTION98
1.6766-1.73070.12611900.10473798X-RAY DIFFRACTION99
1.7307-1.79250.14861870.10873804X-RAY DIFFRACTION99
1.7925-1.86430.14421980.1163819X-RAY DIFFRACTION99
1.8643-1.94910.14351670.11723846X-RAY DIFFRACTION99
1.9491-2.05190.1411890.11923831X-RAY DIFFRACTION99
2.0519-2.18050.14262210.11823828X-RAY DIFFRACTION99
2.1805-2.34880.12942110.12183845X-RAY DIFFRACTION100
2.3488-2.58510.14262020.12973870X-RAY DIFFRACTION99
2.5851-2.95910.16332090.14723883X-RAY DIFFRACTION99
2.9591-3.72780.15821890.15053950X-RAY DIFFRACTION99
3.7278-41.58820.19512260.17964051X-RAY DIFFRACTION99

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