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- PDB-3dpm: Structure of mature CPAF complexed with lactacystin -

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Basic information

Entry
Database: PDB / ID: 3dpm
TitleStructure of mature CPAF complexed with lactacystin
ComponentsProtein CT_858
KeywordsTRANSFERASE / cpaf / lactacystin / complex / 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 / PDZ domain / Pdz3 Domain / ClpP/crotonase-like domain superfamily / PDZ superfamily ...Histone Acetyltransferase; Chain A - #70 / 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 / Histone Acetyltransferase; Chain A / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-LAS / Protein CT_858
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5434
Polymers130,7902
Non-polymers7532
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-29 kcal/mol
Surface area42020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.640, 112.070, 164.130
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 Protein CT_858 / cpaf


Mass: 65394.832 Da / Num. of mol.: 2 / Fragment: UNP residues 25-601
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
#2: Chemical ChemComp-LAS / N-acetyl-S-({(2R,3S,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxopyrrolidin-2-yl}carbonyl)cysteine / LACTACYSTIN


Mass: 376.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsIN SOLUTION, LACTACYSTIN IS IN EQUILIBRATION WITH ITS HYDROLIZED PRODUCT OMURALIDE BY REMOVING THE ...IN SOLUTION, LACTACYSTIN IS IN EQUILIBRATION WITH ITS HYDROLIZED PRODUCT OMURALIDE BY REMOVING THE N-ACETYL CYSTEIN PORTION. THE LATTER IS DIRECTLY RESPONSIBLE FOR INHIBITING CPAF. THAT IS WHY SEVERAL ATOMS ARE MISSING IN THIS COORDINATES.

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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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15.0% PEG 4000 (v/v), 0.6M MgCl2, 0.1M Tirs, pH 8.5, 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: 2.35→99 Å / Num. all: 49637 / Num. obs: 47963 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8

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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: 2.35→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.2592 1472 RANDOM
Rwork0.2302 --
obs0.2302 47281 -
all-47376 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.613 Å20 Å20 Å2
2---9.076 Å20 Å2
3---3.463 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8220 0 30 309 8559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.434
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_it1.366
X-RAY DIFFRACTIONc_mcangle_it2.248
X-RAY DIFFRACTIONc_scbond_it2.301
X-RAY DIFFRACTIONc_scangle_it3.488

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