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- PDB-4ql6: Structure of C. trachomatis CT441 -

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Basic information

Entry
Database: PDB / ID: 4ql6
TitleStructure of C. trachomatis CT441
ComponentsCarboxy-terminal processing protease
KeywordsHYDROLASE / Ser/Lys/Gln catalytic triad / Protease / Chaperone
Function / homology
Function and homology information


serine-type peptidase activity
Similarity search - Function
Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Carboxy-terminal processing protease / Carboxy-terminal processing protease
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.97 Å
AuthorsKohlmann, F. / Hilgenfeld, R. / Hansen, G.
CitationJournal: J.Bacteriol. / Year: 2015
Title: Structural basis of the proteolytic and chaperone activity of Chlamydia trachomatis CT441
Authors: Kohlmann, F. / Shima, K. / Hilgenfeld, R. / Solbach, W. / Rupp, J. / Hansen, G.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Other
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxy-terminal processing protease
B: Carboxy-terminal processing protease
C: Carboxy-terminal processing protease


Theoretical massNumber of molelcules
Total (without water)215,8433
Polymers215,8433
Non-polymers00
Water0
1
A: Carboxy-terminal processing protease
C: Carboxy-terminal processing protease


Theoretical massNumber of molelcules
Total (without water)143,8952
Polymers143,8952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-4 kcal/mol
Surface area47840 Å2
MethodPISA
2
B: Carboxy-terminal processing protease

B: Carboxy-terminal processing protease


Theoretical massNumber of molelcules
Total (without water)143,8952
Polymers143,8952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_566x,-y+1,-z+11
Buried area2510 Å2
ΔGint-3 kcal/mol
Surface area48600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.730, 183.990, 209.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Carboxy-terminal processing protease / tail-specific protease CT441


Mass: 71947.625 Da / Num. of mol.: 3 / Mutation: S455A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: L2/434/Bu / Gene: CT441, CTL0700, tsp / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
References: UniProt: B0B813, UniProt: A0A0H3MDM0*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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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: 3.91 Å3/Da / Density % sol: 68.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M 2-(N-morpholino)ethanesulfonic acid, 0.1M manganese sulfate, 5%(v/v) PEG 6000, 6%(v/v) ethylene glycol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.95→33.441 Å / Num. obs: 65713 / % possible obs: 92.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 76.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.5
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 11.5 / Num. unique all: 65713 / % possible all: 92.3

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Processing

Software
NameVersionClassification
MAR345data collection
PHENIXmodel building
BUCCANEERmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.97→33.441 Å / FOM work R set: 0.7652 / SU ML: 0.4 / σ(F): 1.35 / Phase error: 29.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2814 3232 5.05 %random
Rwork0.2558 ---
obs0.2571 64061 91.49 %-
all-70020 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245.75 Å2 / Biso mean: 99.69 Å2 / Biso min: 47.15 Å2
Refinement stepCycle: LAST / Resolution: 2.97→33.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12071 0 0 0 12071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412313
X-RAY DIFFRACTIONf_angle_d0.84916627
X-RAY DIFFRACTIONf_chiral_restr0.0591810
X-RAY DIFFRACTIONf_plane_restr0.0042156
X-RAY DIFFRACTIONf_dihedral_angle_d13.3774611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9697-3.0140.42351220.39092179230177
3.014-3.06110.37211350.36032552268790
3.0611-3.11120.35661320.3362566269890
3.1112-3.16480.34921370.32442590272791
3.1648-3.22230.36531380.31272594273290
3.2223-3.28420.35161330.29722632276592
3.2842-3.35120.28641350.28212558269390
3.3512-3.4240.28621400.28652616275692
3.424-3.50360.27411360.26632659279592
3.5036-3.59110.31911600.27522592275292
3.5911-3.68810.29291450.26262680282593
3.6881-3.79650.29861490.24842631278092
3.7965-3.91880.30171250.24712723284894
3.9188-4.05860.25361290.23752715284494
4.0586-4.22090.21551330.22432698283194
4.2209-4.41250.241370.22482743288094
4.4125-4.64460.23191480.20662716286494
4.6446-4.93480.24321360.2192713284994
4.9348-5.31440.27651470.23712744289193
5.3144-5.84660.31671620.26032693285593
5.8466-6.68680.27651600.26812701286192
6.6868-8.40250.24021400.2522748288892
8.4025-33.44330.29681530.26532786293990
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0803-0.0604-0.1103-0.03610.0530.1760.28180.5473-0.0005-0.51160.2129-0.96290.03240.2447-01.1550.05120.06571.1688-0.24691.6248165.3728145.684227.8851
23.60010.8524-0.7632.57890.12190.4389-0.09910.6013-0.3447-0.32380.1784-0.5519-0.08920.1064-00.7712-0.02260.10020.763-0.01610.5956138.2461143.405236.5753
30.4838-0.17630.19650.20410.13960.3630.1640.01340.2277-0.2861-0.1769-0.0687-0.30090.242400.96230.02960.17040.74290.09610.645739.99486.343752.4624
41.38610.16941.4320.77110.43351.6173-0.0461-0.11180.1275-0.0664-0.05410.0504-0.1754-0.0651-00.7762-0.02130.20350.67350.09380.752550.800694.041477.0396
50.02310.0406-0.0316-0.02350.02510.00810.04880.3654-0.3141-0.786-0.13650.4431-0.0127-0.4407-01.5181-0.19690.09631.7947-0.47782.210468.6893108.858516.8244
62.80130.37280.2862.0703-0.28261.4383-0.2250.7777-0.8911-0.55830.05290.50280.4504-0.2521-00.878-0.07640.25040.9078-0.19071.237290.6284116.02633.6219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 22 THROUGH 97 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 98 THROUGH 644 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 22 THROUGH 97 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 98 THROUGH 644 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 24 THROUGH 97 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 98 THROUGH 644 )

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