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- PDB-6o1z: Structure of pCW3 conjugation coupling protein TcpA hexagonal cry... -

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Basic information

Entry
Database: PDB / ID: 6o1z
TitleStructure of pCW3 conjugation coupling protein TcpA hexagonal 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FtsK/SpoIIIE domain-containing protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA translocase coupling protein


Theoretical massNumber of molelcules
Total (without water)41,1661
Polymers41,1661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.500, 108.500, 148.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein DNA translocase coupling protein


Mass: 41166.328 Da / Num. of mol.: 1
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

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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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25 % (w/v) PEG 3350, 0.1 M NaCitrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→46.98 Å / Num. obs: 9949 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 89.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.038 / Rrim(I) all: 0.143 / Net I/σ(I): 13.7 / Num. measured all: 138765 / Scaling rejects: 101
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
3.1-3.3114.41.1372511617450.8860.311.182.6100
8.77-46.9812.10.04262085130.9990.0120.04440.699.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O1X

6o1x


Resolution: 3.1→46.98 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.457
RfactorNum. reflection% reflectionSelection details
Rfree0.275 492 4.95 %RANDOM
Rwork0.197 ---
obs0.201 9946 99.8 %-
Displacement parametersBiso max: 205.16 Å2 / Biso mean: 115.29 Å2 / Biso min: 60.1 Å2
Baniso -1Baniso -2Baniso -3
1-15.999 Å20 Å20 Å2
2--15.999 Å20 Å2
3----31.998 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.1→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 0 0 2854
Num. residues----360
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1073SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes487HARMONIC5
X-RAY DIFFRACTIONt_it2897HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion387SEMIHARMONIC5
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_contact3397SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2897HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3895HARMONIC21.28
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion23.38
LS refinement shellResolution: 3.1→3.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.3972 20 4.82 %
Rwork0.2182 395 -
all0.2256 415 -
obs--99.29 %
Refinement TLS params.Method: refined / Origin x: 4.6463 Å / Origin y: 32.0675 Å / Origin z: 32.488 Å
111213212223313233
T-0.1742 Å2-0.051 Å2-0.0493 Å2--0.3749 Å2-0.0739 Å2--0.376 Å2
L2.1992 °20.0472 °2-0.1523 °2-1.7755 °2-0.9447 °2--1.032 °2
S0.0278 Å °-0.6363 Å °-0.0324 Å °0.889 Å °-0.1205 Å °0.1128 Å °-0.1323 Å °0.0153 Å °0.0927 Å °
Refinement TLS groupSelection details: { A|* }

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