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- PDB-4mlk: 3.05A resolution structure of CT584 from Chlamydia trachomatis -

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Basic information

Entry
Database: PDB / ID: 4mlk
Title3.05A resolution structure of CT584 from Chlamydia trachomatis
ComponentsCT584 protein
KeywordsUNKNOWN FUNCTION / CT584 / Chlamydia / hypothetical protein
Function / homology
Function and homology information


Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1050 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1130 / CT_584-like / CT_584-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.051 Å
AuthorsHickey, J. / Lovell, S. / Kemege, K. / Barta, M.L. / Battaile, K.P. / Hefty, P.S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of CT584 from Chlamydia trachomatis refined to 3.05 angstrom resolution.
Authors: Barta, M.L. / Hickey, J. / Kemege, K.E. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CT584 protein


Theoretical massNumber of molelcules
Total (without water)22,4501
Polymers22,4501
Non-polymers00
Water00
1
A: CT584 protein
x 6


Theoretical massNumber of molelcules
Total (without water)134,6996
Polymers134,6996
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area24530 Å2
ΔGint-243 kcal/mol
Surface area43720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.236, 112.236, 82.072
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein CT584 protein


Mass: 22449.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: L2/434/Bu / Gene: CTL0847 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0B8F8, UniProt: A0A0H3MCR9*PLUS

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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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 30% (w/v) PEG 8000, 0.05M sodium cacodylate 0.2M ammonium acetate, 0.01M magnesium acetate, pH 8.5, 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: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.051→62.708 Å / Num. all: 3900 / Num. obs: 3900 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 75.53 Å2 / Rsym value: 0.093 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.05-3.2110.50.7131.158125510.713100
3.21-3.4110.40.4051.955475320.405100
3.41-3.6510.20.2772.750654950.277100
3.65-3.949.90.1714.446604720.171100
3.94-4.319.20.0868.739634290.086100
4.31-4.829.60.05712.637673930.057100
4.82-5.579.50.05912.633233500.059100
5.57-6.8210.50.0661131072960.066100
6.82-9.6410.20.03714.524442390.037100
9.64-62.7088.70.0321812381430.03299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.05 Å62.71 Å
Translation3.05 Å62.71 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementResolution: 3.051→32.4 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 1.72 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 178 4.57 %
Rwork0.2253 3717 -
obs0.2267 3895 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.24 Å2 / Biso mean: 75.3667 Å2 / Biso min: 25.93 Å2
Refinement stepCycle: LAST / Resolution: 3.051→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 0 0 1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071260
X-RAY DIFFRACTIONf_angle_d1.0741691
X-RAY DIFFRACTIONf_chiral_restr0.05195
X-RAY DIFFRACTIONf_plane_restr0.006218
X-RAY DIFFRACTIONf_dihedral_angle_d16.273474
LS refinement shellResolution: 3.0507→32.4016 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2529 178 -
Rwork0.2253 3717 -
all-3895 -
obs--100 %

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