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- PDB-1gl6: Plasmid coupling protein TrwB in complex with the non-hydrolysabl... -

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Basic information

Entry
Database: PDB / ID: 1gl6
TitlePlasmid coupling protein TrwB in complex with the non-hydrolysable GTP analogue GDPNP
ComponentsATPASE
KeywordsCOUPLING PROTEIN / TYPE IV SECRETION SYSTEM / BACTERIAL CONJUG PROTEIN / RING HELICASE
Function / homology
Function and homology information


nucleotide binding / metal ion binding / identical protein binding / plasma membrane
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / TrwB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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.X. / Moncalian, G. / De La Cruz, F. / Coll, M.
History
DepositionAug 28, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: ATPASE
B: ATPASE
D: ATPASE
E: ATPASE
F: ATPASE
G: ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,27915
Polymers291,3506
Non-polymers3,9299
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)151.600, 151.600, 252.000
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
ATPASE


Mass: 48558.312 Da / Num. of mol.: 6 / Fragment: CYTOSOLIC FRAGMENT / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH GDPNP. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04230
#2: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: ID14-2 / Wavelength: 0.842
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.842 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 81160 / % possible obs: 98 % / Redundancy: 5.3 % / Biso Wilson estimate: 76.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.7 / % possible all: 92

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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: 2.8→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FREE RFACTOR USED UNTIL PENULTIMATE REFINEMENT CYCLE. SAME INDICES AS IN 1E9R, 1GKI AND 1GL7.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 -7 %RANDOM
Rwork0.214 ---
obs0.214 81037 100 %-
Displacement parametersBiso mean: 56 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19612 0 240 589 20441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.42
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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