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- PDB-3dpn: Crystal Structure of cpaf s499a mutant -

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Basic information

Entry
Database: PDB / ID: 3dpn
TitleCrystal Structure of cpaf s499a mutant
ComponentsProtein CT_858
KeywordsTRANSFERASE / cpaf / s499a / zymogen
Function / homology
Function and homology information


serine-type peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / signal transduction / proteolysis
Similarity search - Function
Chlamydial protease/proteasome-like activity factor, PDZ domain / PDZ domain / tail specific protease / Tail specific protease / Peptidase family S41 / PDZ domain / Pdz3 Domain / ClpP/crotonase-like domain superfamily / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChai, J. / Huang, Z.
CitationJournal: Cell Host Microbe / Year: 2008
Title: Structural basis for activation and inhibition of the secreted chlamydia protease CPAF
Authors: Huang, Z. / Feng, Y. / Chen, D. / Wu, X. / Huang, S. / Wang, X. / Xiao, X. / Li, W. / Huang, N. / Gu, L. / Zhong, G. / Chai, J.
History
DepositionJul 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CT_858
B: Protein CT_858


Theoretical massNumber of molelcules
Total (without water)130,7582
Polymers130,7582
Non-polymers00
Water00
1
A: Protein CT_858


Theoretical massNumber of molelcules
Total (without water)65,3791
Polymers65,3791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein CT_858


Theoretical massNumber of molelcules
Total (without water)65,3791
Polymers65,3791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.670, 192.670, 338.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Protein CT_858 / cpaf


Mass: 65378.832 Da / Num. of mol.: 2 / Fragment: UNP residues 25-601 / Mutation: S499A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Plasmid: PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 / References: UniProt: O84866

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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: 4.63 Å3/Da / Density % sol: 73.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.9M NaNO3, 0.5M NaCl, 0.08M KCl, 0.1M Bis-Tris propane (BTP), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 2007
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→99 Å / Num. obs: 39050 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Rsym value: 0.052 / Net I/σ(I): 16.2
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DOR

3dor


Resolution: 3.3→20 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1800 4.9 %RANDOM
Rwork0.257 34499 --
obs-36299 99.6 %-
Solvent computationBsol: 43.375 Å2
Displacement parametersBiso max: 197.76 Å2 / Biso mean: 106.88 Å2 / Biso min: 19.71 Å2
Baniso -1Baniso -2Baniso -3
1--24.696 Å2-30.891 Å20 Å2
2---24.696 Å20 Å2
3---49.392 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8476 0 0 0 8476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.676
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

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