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- PDB-6o1w: Structure of pCW3 conjugation coupling protein TcpA monomer ortho... -

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Basic information

Entry
Database: PDB / ID: 6o1w
TitleStructure of pCW3 conjugation coupling protein TcpA monomer orthorhombic crystal form
ComponentsDNA translocase coupling protein
KeywordsTRANSLOCASE / ATPase / Conjugation
Function / homology
Function and homology information


DNA binding / ATP binding / identical protein binding / membrane
Similarity search - Function
FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
beta-D-glucopyranose / Probable DNA translocase coupling protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsTraore, D.A.K. / Ahktar, N. / Torres, V.T. / Adams, V. / Coulibaly, F. / Panjikar, S. / Caradoc-Davies, T.T. / Rood, J.I. / Whisstock, J.C.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1104502 Australia
CitationJournal: To be published
Title: Structure of pCW3 conjugation coupling protein TcpA
Authors: Traore, D.A.K. / Whisstock, J.C.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA translocase coupling protein
B: DNA translocase coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8897
Polymers80,9882
Non-polymers9015
Water6,017334
1
A: DNA translocase coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0344
Polymers40,4941
Non-polymers5403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA translocase coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8543
Polymers40,4941
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.170, 101.830, 140.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA translocase coupling protein


Mass: 40493.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: tcpA, pCW3_0030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PLI0
#2: Sugar
ChemComp-BGC / beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 20 % (W/V) PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→47.85 Å / Num. obs: 39456 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 39.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.036 / Rrim(I) all: 0.126 / Net I/σ(I): 13.6 / Num. measured all: 470099 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2712.30.8314142733560.870.2430.8663.399.7
9.07-47.8510.40.06568696580.9970.020.06834.199.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata scaling
SHELXphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→42.43 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.254 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1936 4.91 %RANDOM
Rwork0.179 ---
obs0.182 39392 99.9 %-
Displacement parametersBiso max: 136.69 Å2 / Biso mean: 44.61 Å2 / Biso min: 16.72 Å2
Baniso -1Baniso -2Baniso -3
1--6.2361 Å20 Å20 Å2
2--2.3504 Å20 Å2
3---3.8857 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 2.2→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 120 334 6002
Biso mean--80 54.56 -
Num. residues----702
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2131SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes945HARMONIC5
X-RAY DIFFRACTIONt_it5754HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion779SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6597SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5754HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7791HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion18.18
LS refinement shellResolution: 2.2→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3216 31 3.93 %
Rwork0.1903 757 -
all0.195 788 -
obs--98.24 %
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)
10.19040.14920.01330.54-0.57751.12680.0237-0.0022-0.0203-0.0011-0.03460.02440.0950.02740.0108-0.0356-0.0107-0.0029-0.03140.0006-0.0395-16.77576.257107.12
20.85740.8281-0.35090.7749-0.14270.4878-0.0334-0.0594-0.1431-0.0785-0.0138-0.15950.0290.05960.0472-0.09390.0150.0069-0.04130.0025-0.006314.54319.9873127.864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A106 - 458
2X-RAY DIFFRACTION2{ B|* }B110 - 458

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