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- PDB-6o1y: Structure of pCW3 conjugation coupling protein TcpA monomeric for... -

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Basic information

Entry
Database: PDB / ID: 6o1y
TitleStructure of pCW3 conjugation coupling protein TcpA monomeric form with ATP
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
ADENOSINE-5'-TRIPHOSPHATE / beta-D-glucopyranose / Probable DNA translocase coupling protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
B: DNA translocase coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5594
Polymers80,8712
Non-polymers6872
Water4,234235
1
A: DNA translocase coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1233
Polymers40,4361
Non-polymers6872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA translocase coupling protein


Theoretical massNumber of molelcules
Total (without water)40,4361
Polymers40,4361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.453, 108.663, 142.384
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: 40435.590 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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 % (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→47.96 Å / Num. obs: 23633 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 65.88 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.253 / Rpim(I) all: 0.101 / Rrim(I) all: 0.273 / Net I/σ(I): 8.2 / Num. measured all: 169943 / Scaling rejects: 4
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
2.7-2.837.32.2732229830710.30.8952.445198.7
8.94-47.965.90.03343447350.9990.0150.03737.799.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O1W

6o1w


Resolution: 2.7→43.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.35
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1165 4.94 %RANDOM
Rwork0.181 ---
obs0.185 23578 99.8 %-
Displacement parametersBiso max: 154.94 Å2 / Biso mean: 62.39 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.4049 Å20 Å20 Å2
2---8.2898 Å20 Å2
3---7.885 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.7→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 67 235 5908
Biso mean--98.58 50.67 -
Num. residues----708
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2129SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes974HARMONIC5
X-RAY DIFFRACTIONt_it5761HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion769SEMIHARMONIC5
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_contact6710SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5761HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7775HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion22.74
LS refinement shellResolution: 2.7→2.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2864 26 5.51 %
Rwork0.234 446 -
all0.2369 472 -
obs--90.91 %
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)
10.2618-0.23820.3611.213-0.61512.0789-0.010.0576-0.0384-0.145-0.07510.09410.2344-0.2340.0851-0.2416-0.07430.01290.2215-0.0564-0.1221-16.37846.706-32.7269
21.28290.7569-0.35831.061-0.14620.8725-0.07740.07620.0024-0.04940.0493-0.07780.09760.020.028-0.18240.0197-0.01240.0837-0.0227-0.079-37.985920.9032-11.8036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A106 - 458
2X-RAY DIFFRACTION2{ B|* }B105 - 459

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