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- PDB-4ilo: 2.12A resolution structure of CT398 from Chlamydia trachomatis -

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Basic information

Entry
Database: PDB / ID: 4ilo
Title2.12A resolution structure of CT398 from Chlamydia trachomatis
ComponentsCT398
KeywordsUNKNOWN FUNCTION / hypothetical protein / DNA/RNA binding / coiled-coil / Zn ribbon domain / structural proteomics
Function / homologyC4-type zinc ribbon domain / C4-type zinc ribbon domain / Helix Hairpins - #1490 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / metal ion binding / zf-RING_7 domain-containing protein / zf-RING_7 domain-containing protein
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsBarta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
CitationJournal: To be Published
Title: 2.12A resolution structure of CT398 from Chlamydia trachomatis
Authors: Barta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: CT398
B: CT398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9435
Polymers59,7502
Non-polymers1933
Water3,549197
1
A: CT398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0033
Polymers29,8751
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CT398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9402
Polymers29,8751
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: CT398
B: CT398
hetero molecules

A: CT398
B: CT398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,88610
Polymers119,5004
Non-polymers3866
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area9120 Å2
ΔGint-23 kcal/mol
Surface area52490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.345, 92.634, 82.652
Angle α, β, γ (deg.)90.000, 95.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-503-

HOH

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Components

#1: Protein CT398


Mass: 29875.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: 434/Bu / ATCC VR-902B / Gene: CTL0655 / Plasmid: pTBSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0B7W8, UniProt: A0A0H3MH91*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 4.0, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.283 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2012
RadiationMonochromator: Si(111) / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.12→82.255 Å / Num. all: 37617 / Num. obs: 36767 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 30.54 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.8
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2973 / Rsym value: 0.595 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1112refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.12→41.128 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7934 / SU ML: 0.27 / σ(F): 1.34 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1829 5.01 %RANDOM
Rwork0.2012 ---
obs0.2032 36746 93.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.9 Å2 / Biso mean: 31.4771 Å2 / Biso min: 4.79 Å2
Refinement stepCycle: LAST / Resolution: 2.12→41.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3755 0 6 197 3958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123805
X-RAY DIFFRACTIONf_angle_d1.1135100
X-RAY DIFFRACTIONf_chiral_restr0.066589
X-RAY DIFFRACTIONf_plane_restr0.006674
X-RAY DIFFRACTIONf_dihedral_angle_d16.1641495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.12-2.14910.35361270.31282684281195
2.1491-2.17980.33921680.30092589275794
2.1798-2.21230.34411280.29592721284995
2.2123-2.24690.31811270.29492608273593
2.2469-2.28370.33331360.28782572270892
2.2837-2.32310.32561170.27292463258089
2.3231-2.36530.30581250.25132419254485
2.3653-2.41080.30991490.25042559270893
2.4108-2.460.28331410.24452733287494
2.46-2.51350.25381370.22632459259690
2.5135-2.5720.23961200.21642676279694
2.572-2.63630.32341310.22132688281995
2.6363-2.70760.25621040.21822683278795
2.7076-2.78720.25651360.22082723285995
2.7872-2.87720.24321390.21172659279896
2.8772-2.980.25071540.21732691284596
2.98-3.09920.24631620.22352683284596
3.0992-3.24020.26591600.22122600276094
3.2402-3.4110.25051360.20732534267090
3.411-3.62460.22641350.1872735287097
3.6246-3.90420.24861580.16552639279794
3.9042-4.29680.18811700.16062737290798
4.2968-4.91760.20521320.14362738287096
4.9176-6.19230.1991320.18832575270792
6.1923-41.13540.15751480.14662694284295

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