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- PDB-2cc3: Structure of Agrobacterium tumefaciens VirB8 protein -

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Basic information

Entry
Database: PDB / ID: 2cc3
TitleStructure of Agrobacterium tumefaciens VirB8 protein
ComponentsPROTEIN VIRB8
KeywordsSECRETION SYSTEM / VIRB8 / AGROBACTERIUM / TYPE IV SECRETION SYSTEM / CONSURF
Function / homology
Function and homology information


type IV secretion system complex / protein secretion by the type IV secretion system / identical protein binding / plasma membrane
Similarity search - Function
VirB8 protein / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesAGROBACTERIUM TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBailey, S. / Ward, D. / Middleton, R. / Grossmann, G. / Zambryski, P.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Agrobacterium Tumefaciens Virb8 Structure Reveals Potential Protein-Protein Interactions Sites.
Authors: Bailey, S. / Ward, D. / Middleton, R. / Grossmann, J.G. / Zambryski, P.C.
History
DepositionJan 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2006Provider: 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 / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN VIRB8
B: PROTEIN VIRB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9444
Polymers33,7072
Non-polymers2362
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.269, 72.349, 48.844
Angle α, β, γ (deg.)90.00, 110.66, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 3 / Auth seq-ID: 91 - 227 / Label seq-ID: 4 - 140

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.76768, 0.02161, 0.64047), (0.03444, -0.99938, -0.00757), (0.6399, 0.02787, -0.76795)
Vector: -2.07703, 6.8943, 5.1655)

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Components

#1: Protein PROTEIN VIRB8


Mass: 16853.740 Da / Num. of mol.: 2 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 92-237
Source method: isolated from a genetically manipulated source
Details: RESIDUES 88-91 ARE FROM TAG AND RESIDUES 92-231 CORRESPOND TO VIRB8
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Strain: PTIC58 / Plasmid: PDW134 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17798
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 88-91 ARE INSERTED TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.6
Details: 0.1 M SODIUM ACETATE, PH 4.6, 0.2 M SODIUM BROMIDE, 20% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17972 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.3 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BHM

2bhm


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.818 / SU B: 7.736 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.301 928 5.2 %RANDOM
Rwork0.235 ---
obs0.239 17010 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20.33 Å2
2---0.25 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 16 171 2477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222358
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9523218
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81723.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.25515374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2171518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021816
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.21118
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21588
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5921474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.72732350
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.95221009
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2483868
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 548 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.060.05
loose positional0.65
tight thermal0.170.5
loose thermal2.3510
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 66
Rwork0.283 1118

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