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- PDB-4gqm: Crystal structure of a helix-turn-helix containing hypothetical p... -

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Basic information

Entry
Database: PDB / ID: 4gqm
TitleCrystal structure of a helix-turn-helix containing hypothetical protein (CT009) from Chlamydia trachomatis in a sub-domain swap conformation
ComponentsCT009
KeywordsUNKNOWN FUNCTION / helix-turn-helix
Function / homology
Function and homology information


membrane => GO:0016020 / DNA binding
Similarity search - Function
Helix-turn-helix domain / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsKemege, K. / Hickey, J. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
CitationJournal: To be Published
Title: Crystal structure of a helix-turn-helix containing hypothetical protein (CT009) from Chlamydia trachomatis in a sub-domain swap conformation
Authors: Kemege, K. / Hickey, J. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
History
DepositionAug 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: 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
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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CT009


Theoretical massNumber of molelcules
Total (without water)13,3911
Polymers13,3911
Non-polymers00
Water2,000111
1
A: CT009

A: CT009


Theoretical massNumber of molelcules
Total (without water)26,7832
Polymers26,7832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4940 Å2
ΔGint-57 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.171, 55.171, 88.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CT009


Mass: 13391.338 Da / Num. of mol.: 1 / Fragment: UNP residues 1-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: L2/434/Bu / Gene: CTL0264 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0B9B6, UniProt: A0A0H3MGJ5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 30% w/v PEG4000, 0.1 M Tris, pH 8.5, 0.2 M magnesium chloride, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→46.762 Å / Num. obs: 38420 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 25.1
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.5 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIXdev_1096refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COMPUTATIONAL MODEL GENERATED FROM THE PROGRAM MODELLER

Resolution: 1.25→29.208 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 14.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1731 1921 5.01 %RANDOM
Rwork0.1585 ---
obs0.1592 38338 99.92 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.78 Å2 / Biso mean: 20.238 Å2 / Biso min: 9.18 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms837 0 0 111 948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121036
X-RAY DIFFRACTIONf_angle_d1.4371408
X-RAY DIFFRACTIONf_chiral_restr0.083155
X-RAY DIFFRACTIONf_plane_restr0.007185
X-RAY DIFFRACTIONf_dihedral_angle_d13.102410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.28150.28381420.23692536267899
1.2815-1.31620.21541530.194225312684100
1.3162-1.35490.19181220.166325662688100
1.3549-1.39860.18461330.148925702703100
1.3986-1.44860.16831430.142825382681100
1.4486-1.50660.17331240.138225852709100
1.5066-1.57520.151320.118825772709100
1.5752-1.65820.14251530.119525612714100
1.6582-1.76210.1661300.130226022732100
1.7621-1.89810.17091480.136825962744100
1.8981-2.08910.15561370.144825902727100
2.0891-2.39120.17251520.138326332785100
2.3912-3.01220.16541170.172226932810100
3.0122-29.21590.18291350.177928392974100

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