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- PDB-1gki: Plasmid coupling protein TrwB in complex with ADP and Mg2+. -

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Basic information

Entry
Database: PDB / ID: 1gki
TitlePlasmid coupling protein TrwB in complex with ADP and Mg2+.
ComponentsCONJUGAL TRANSFER PROTEIN TRWB
KeywordsCOUPLING PROTEIN / BACTERIAL CONJUGATION / F1-ATPASE-LIKE QUATERNARY STRUCTURE / RING HELICASES
Function / homology
Function and homology information


nucleotide binding / membrane / identical protein binding
Similarity search - Function
Type IV secretion system coupling protein TraD, DNA-binding domain / Type IV secretion-system coupling protein DNA-binding domain / Magnesium chelatase subunit I, C-Terminal domain / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TrwB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGomis-Ruth, F.X. / Moncalian, G. / De La cruz, F. / Coll, M.
Citation
Journal: Nature / Year: 2001
Title: The Bacterial Conjugation Protein Trwb Resembles Ring Helicases and F1-ATPase
Authors: Gomis-Ruth, F.X. / Moncalian, G. / Perez-Luque, R. / Gonzalez, A. / Cabezon, E. / De La Cruz, F. / Coll, M.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Conjugative Plasmid Protein Trwb, an Integral Membrane Type Iv Secretion System Coupling Protein: Detailed Structural Features and Mapping of the Active Site Cleft.
Authors: Gomis-Ruth, F. / Moncalian, G. / De La Cruz, F. / Coll, M.
History
DepositionAug 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CONJUGAL TRANSFER PROTEIN TRWB
B: CONJUGAL TRANSFER PROTEIN TRWB
D: CONJUGAL TRANSFER PROTEIN TRWB
E: CONJUGAL TRANSFER PROTEIN TRWB
F: CONJUGAL TRANSFER PROTEIN TRWB
G: CONJUGAL TRANSFER PROTEIN TRWB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,19019
Polymers292,0296
Non-polymers3,16113
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)151.100, 151.100, 251.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
CONJUGAL TRANSFER PROTEIN TRWB / ATPASE


Mass: 48671.469 Da / Num. of mol.: 6 / Fragment: CYTOSOLIC, RESIDUES 71-507 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH ADP AND MG2+. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04230
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, D, E, F, G FIRST 70 RESIDUES DELETED

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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.033
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→51.3 Å / Num. obs: 67169 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 66.6 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 5.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E9R

1e9r


Resolution: 3→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FREE RFACTOR USED UNTIL PENULTIMATE REFINEMENT CYCLE. THERE IS NCS IN THE A.U. THE SIX PROTEIN CHAINS (A-G) ARE CHEMICALLY IDENTICAL. SOME N- AND C-TERMINAL RESIDUES ARE DISORDERED AND HAVE NOT BEEN TRACED.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 -7 %RANDOM
Rwork0.21 ---
obs0.21 67164 100 %-
Displacement parametersBiso mean: 49.6 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19536 0 197 417 20150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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