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- PDB-7km3: Dodecameric Structure of the Chlamydia trachomatis Flavin Prenylt... -

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Basic information

Entry
Database: PDB / ID: 7km3
TitleDodecameric Structure of the Chlamydia trachomatis Flavin Prenyltransferase UbiX Ortholog CT220 with FMN and DMAP
ComponentsFlavin prenyltransferase UbiX
KeywordsTRANSFERASE / Chlamydia
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / carboxy-lyase activity
Similarity search - Function
Flavin prenyltransferase UbiX-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein
Similarity search - Domain/homology
Dimethylallyl monophosphate / FLAVIN MONONUCLEOTIDE / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsNguyen, T. / Nicely, N.I. / Belaia-Martiniouk, A. / Dunne, A.P. / McCafferty, D.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI107951 United States
CitationJournal: To be published
Title: Functional and structural validation of CT220 as the UbiX-like flavin prenyltransferase from Chlamydial menaquinone biosynthesis
Authors: Nguyen, T. / Nicely, N.I. / Belaia-Martiniouk, A. / Dunne, A.P. / McCafferty, D.G.
History
DepositionNov 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Flavin prenyltransferase UbiX
I: Flavin prenyltransferase UbiX
A: Flavin prenyltransferase UbiX
B: Flavin prenyltransferase UbiX
C: Flavin prenyltransferase UbiX
D: Flavin prenyltransferase UbiX
E: Flavin prenyltransferase UbiX
F: Flavin prenyltransferase UbiX
G: Flavin prenyltransferase UbiX
H: Flavin prenyltransferase UbiX
J: Flavin prenyltransferase UbiX
K: Flavin prenyltransferase UbiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,20036
Polymers263,73012
Non-polymers7,46924
Water9,458525
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.270, 151.224, 167.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 71 or resid 83 through 186))
d_2ens_1(chain "B" and (resid 2 through 71 or resid 83 through 186))
d_3ens_1(chain "C" and (resid 2 through 71 or resid 83 through 186))
d_4ens_1(chain "D" and (resid 2 through 71 or resid 83 through 186))
d_5ens_1(chain "E" and (resid 2 through 71 or resid 83 through 186))
d_6ens_1(chain "F" and (resid 2 through 71 or resid 83 through 186))
d_7ens_1(chain "G" and (resid 2 through 71 or resid 83 through 186))
d_8ens_1(chain "H" and (resid 2 through 71 or resid 83 through 186))
d_9ens_1(chain "I" and (resid 2 through 71 or resid 83 through 186))
d_10ens_1(chain "J" and (resid 2 through 71 or resid 83 through 186))
d_11ens_1(chain "K" and (resid 2 through 71 or resid 83 through 186))
d_12ens_1(chain "L" and (resid 2 through 71 or resid 83 through 186))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSSERC2 - 71
d_12ens_1ILELYSC80 - 183
d_21ens_1LYSSERD2 - 71
d_22ens_1ILELYSD79 - 182
d_31ens_1LYSSERE2 - 71
d_32ens_1ILELYSE83 - 186
d_41ens_1LYSSERF2 - 71
d_42ens_1ILELYSF83 - 186
d_51ens_1LYSSERG2 - 71
d_52ens_1ILELYSG79 - 182
d_61ens_1LYSSERH2 - 71
d_62ens_1ILELYSH83 - 186
d_71ens_1LYSSERI2 - 71
d_72ens_1ILELYSI78 - 181
d_81ens_1LYSSERJ2 - 71
d_82ens_1ILELYSJ79 - 182
d_91ens_1LYSSERB2 - 71
d_92ens_1ILELYSB73 - 176
d_101ens_1LYSSERK2 - 71
d_102ens_1ILELYSK83 - 186
d_111ens_1LYSSERL2 - 71
d_112ens_1ILELYSL83 - 186
d_121ens_1LYSSERA1 - 70
d_122ens_1ILELYSA72 - 175

NCS oper:
IDCodeMatrixVector
1given(-0.393871468361, 0.833656878723, 0.387145289224), (-0.135230789415, 0.364051849642, -0.921509025657), (-0.909163296666, -0.415310076123, -0.0306535587671)-57.7079877497, -18.0911073963, -55.0597972372
2given(0.963435192835, 0.0576503382207, 0.26166594679), (0.257765907156, -0.46599503147, -0.84640732969), (0.0731393622799, 0.882907169043, -0.463816304734)2.04033901495, 1.65234555119, -20.7599017919
3given(-0.095635316685, -0.124472178079, -0.987603444246), (-0.125518883149, -0.982723654457, 0.136011870597), (-0.987470959662, 0.136970419634, 0.0783594791323)-62.9409281916, 0.935218664735, -57.3213308102
4given(-0.615920608307, 0.726722774482, 0.304164122329), (0.7371262323, 0.395366843421, 0.548023700929), (0.278004895494, 0.561746444735, -0.779201007384)-68.4505501695, 41.9768684775, -15.7816861265
5given(-0.433170769832, -0.765799604337, 0.475304165941), (0.89398763426, -0.432144781434, 0.118477836194), (0.114669934825, 0.476237182375, 0.871807864251)-53.7365540118, 43.9977396121, 2.02478283314
6given(-0.155777451317, -0.824432788593, 0.544099221423), (-0.37529050275, 0.55891702952, 0.739438160131), (-0.913723384951, -0.0890074783617, -0.396468466071)-40.4313950795, -4.62317205305, -61.5038083416
7given(-0.317143588749, -0.656402084199, 0.684511685784), (-0.615630617182, -0.406538748961, -0.675074209833), (0.721400642711, -0.635501809166, -0.275170062404)-45.9777214304, -34.2114102594, 14.0709026521
8given(0.967502935831, 0.251237286842, 0.028598861127), (0.0938655686053, -0.461868092849, 0.881967754421), (0.234792087149, -0.85062194335, -0.470441266582)-1.89829144281, 21.270826064, -10.525657748
9given(-0.168618575687, -0.355290803245, -0.919421677503), (-0.828559701104, 0.556341496645, -0.0630314272199), (0.533906918517, 0.751167480819, -0.388189152501)-64.1279284887, -36.7468455107, 0.885408701695
10given(-0.35262283116, -0.143243409181, -0.924736970533), (0.85407905287, 0.354534336169, -0.380597393483), (0.382369076147, -0.924005806369, -0.00267570611969)-72.7881188519, 33.1672992148, 3.5578764157
11given(-0.473781164725, 0.873905264499, 0.108724406793), (-0.746725048629, -0.464107674349, 0.476451223485), (0.466833064062, 0.144546377648, 0.872452425641)-65.4359986121, -22.7223177388, 18.4579069066

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Components

#1: Protein
Flavin prenyltransferase UbiX


Mass: 21977.537 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria)
Strain: D/UW-3/Cx / Gene: ubiX, CT_220 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O84222, flavin prenyltransferase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-4LR / Dimethylallyl monophosphate


Mass: 166.112 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H11O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 200mM Magnesium Acetate Tetrahydrate, 20% PEG-3350 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 107415 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.067 / Χ2: 1.49 / Net I/σ(I): 26.2
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5295 / CC1/2: 0.903 / Χ2: 1.09 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zaf

4zaf


Resolution: 2.26→43.58 Å / SU ML: 0.3048 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.5766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 2000 1.86 %
Rwork0.1996 105304 -
obs0.2004 107304 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.04 Å2
Refinement stepCycle: LAST / Resolution: 2.26→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16822 0 492 525 17839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008617629
X-RAY DIFFRACTIONf_angle_d1.063124103
X-RAY DIFFRACTIONf_chiral_restr0.06442986
X-RAY DIFFRACTIONf_plane_restr0.00622923
X-RAY DIFFRACTIONf_dihedral_angle_d20.19656399
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.539225045159
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.517635641245
ens_1d_4CX-RAY DIFFRACTIONTorsion NCS0.627884810621
ens_1d_5CX-RAY DIFFRACTIONTorsion NCS0.623182030352
ens_1d_6CX-RAY DIFFRACTIONTorsion NCS0.493532528515
ens_1d_7CX-RAY DIFFRACTIONTorsion NCS0.612416901269
ens_1d_8CX-RAY DIFFRACTIONTorsion NCS0.633559758581
ens_1d_9CX-RAY DIFFRACTIONTorsion NCS0.769779573205
ens_1d_10CX-RAY DIFFRACTIONTorsion NCS0.58582453063
ens_1d_11CX-RAY DIFFRACTIONTorsion NCS0.569700862693
ens_1d_12CX-RAY DIFFRACTIONTorsion NCS0.663688729488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.310.37351300.28426868X-RAY DIFFRACTION92.18
2.31-2.380.28421420.25187479X-RAY DIFFRACTION99.97
2.38-2.450.31981430.24777492X-RAY DIFFRACTION100
2.45-2.530.30891410.24667470X-RAY DIFFRACTION99.99
2.53-2.620.2961430.24197501X-RAY DIFFRACTION100
2.62-2.720.27981420.2417507X-RAY DIFFRACTION99.93
2.72-2.840.29481440.23887520X-RAY DIFFRACTION99.96
2.84-2.990.30321420.23637506X-RAY DIFFRACTION99.99
2.99-3.180.3171440.22597545X-RAY DIFFRACTION99.94
3.18-3.430.25951440.22157569X-RAY DIFFRACTION99.95
3.43-3.770.26271440.20417577X-RAY DIFFRACTION99.96
3.77-4.320.19131440.16457648X-RAY DIFFRACTION99.96
4.32-5.440.1731460.14927676X-RAY DIFFRACTION99.96
5.44-43.580.17651510.16367946X-RAY DIFFRACTION99.82

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