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- PDB-3dja: Crystal Structure of cpaf solved with MAD -

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Basic information

Entry
Database: PDB / ID: 3dja
TitleCrystal Structure of cpaf solved with MAD
ComponentsProtein CT_858
KeywordsTRANSFERASE / cpaf / mad / active / dimer
Function / homology
Function and homology information


serine-type peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / signal transduction / proteolysis
Similarity search - Function
Histone Acetyltransferase; Chain A - #70 / Chlamydial protease/proteasome-like activity factor, PDZ domain / PDZ domain / tail specific protease / Tail specific protease / Peptidase family S41 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / PDZ domain / Pdz3 Domain ...Histone Acetyltransferase; Chain A - #70 / Chlamydial protease/proteasome-like activity factor, PDZ domain / PDZ domain / tail specific protease / Tail specific protease / Peptidase family S41 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / PDZ domain / Pdz3 Domain / ClpP/crotonase-like domain superfamily / PDZ superfamily / Histone Acetyltransferase; Chain A / Roll / Alpha-Beta Complex / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 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
DepositionJun 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CT_858
B: Protein CT_858


Theoretical massNumber of molelcules
Total (without water)130,0672
Polymers130,0672
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-30 kcal/mol
Surface area42890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.870, 124.870, 241.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein CT_858 / CPAF


Mass: 65033.473 Da / Num. of mol.: 2 / Fragment: UNP residues 23-601
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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.75M Li2SO4, 0.1M Na Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9641, 0.9792, 0.9793
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Si(111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96411
20.97921
30.97931
ReflectionResolution: 2.59→50 Å / Num. all: 60232 / Num. obs: 60232 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 10.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 30.6
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 9 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5913 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 2184 -RANDOM
Rwork0.2453 ---
obs0.2453 42939 94.9 %-
all-42973 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.326 Å20 Å20 Å2
2---2.326 Å20 Å2
3---4.651 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8290 0 0 0 8290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008293
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.50075
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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