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- PDB-2pt7: Crystal structure of Cag VirB11 (HP0525) and an inhibitory protei... -

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Basic information

Entry
Database: PDB / ID: 2pt7
TitleCrystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)
Components
  • Cag-alfa
  • Hypothetical protein
Keywordshydrolase/protein binding / ATPase / Protein-Protein complex / Type IV secretion / hydrolase-protein binding COMPLEX
Function / homology
Function and homology information


secretion by the type IV secretion system / type IV secretion system complex / nucleotide binding
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #180 / HP1451, C-terminal / HP1451 C-terminal domain / RNA-binding protein KhpB, N-terminal / Jag, N-terminal domain superfamily / RNA-binding protein KhpB / Jag N-terminus / Jag_N / Type IV secretion system protein VirB11 / Beta-Lactamase - #90 ...Ribosomal Protein S8; Chain: A, domain 1 - #180 / HP1451, C-terminal / HP1451 C-terminal domain / RNA-binding protein KhpB, N-terminal / Jag, N-terminal domain superfamily / RNA-binding protein KhpB / Jag N-terminus / Jag_N / Type IV secretion system protein VirB11 / Beta-Lactamase - #90 / Type II/IV secretion system protein / Type II/IV secretion system protein / K homology (KH) domain / Ribosomal Protein S8; Chain: A, domain 1 / GMP Synthetase; Chain A, domain 3 / Beta-Lactamase / K homology domain-like, alpha/beta / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Jag_N domain-containing protein / Cag alpha
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHare, S. / Fischer, W. / Williams, R. / Terradot, L. / Bayliss, R. / Haas, R. / Waksman, G.
CitationJournal: Embo J. / Year: 2007
Title: Identification, structure and mode of action of a new regulator of the Helicobacter pylori HP0525 ATPase.
Authors: Hare, S. / Fischer, W. / Williams, R. / Terradot, L. / Bayliss, R. / Haas, R. / Waksman, G.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Cag-alfa
B: Cag-alfa
C: Cag-alfa
D: Cag-alfa
E: Cag-alfa
F: Cag-alfa
G: Hypothetical protein
H: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)260,9548
Polymers260,9548
Non-polymers00
Water12,376687
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.851, 86.900, 104.129
Angle α, β, γ (deg.)111.04, 95.98, 104.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F
14G
24H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUHOHHOH1AA - I6 - 3316
21LEULEUHOHHOH1DD - L6 - 3316
12LYSLYSHOHHOH1BB - J21 - 33121
22LYSLYSHOHHOH1EE - M21 - 33121
13GLUGLUHOHHOH1CC - K22 - 33122
23GLUGLUHOHHOH1FF - N22 - 33122
14LYSLYSASNASN2GG115 - 2593 - 147
24LYSLYSASNASN2HH115 - 2593 - 147

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Cag-alfa / Cag alpha / VirB11 homolog / Cag pathogenicity island protein


Mass: 37632.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: cag-alfa, cag-alpha / Plasmid: pCDF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7BK04
#2: Protein Hypothetical protein / / HP1451


Mass: 17578.242 Da / Num. of mol.: 2 / Fragment: residue 113-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP1451 / Plasmid: pET 151 D TOPO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O25990
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Mes, 8% polyethylene glycol 8,000, 10mM ethylene-diamine-tetra-acetic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9759 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9759 Å / Relative weight: 1
ReflectionResolution: 2.4→94.916 Å / Num. all: 104768 / Num. obs: 100842 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.243 / % possible all: 96.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å38.56 Å
Translation4 Å38.56 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G6O

1g6o


Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.875 / SU B: 18.036 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26966 5056 5 %RANDOM
Rwork0.22986 ---
obs0.23185 95786 96.27 %-
all-104768 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.827 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.01 Å20.26 Å2
2--0.45 Å20.1 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17207 0 0 687 17894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02217544
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.95223660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60952158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17224.42819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.584153187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.291592
X-RAY DIFFRACTIONr_chiral_restr0.0850.22642
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213100
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.27569
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.211847
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2907
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5891.511077
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92217382
X-RAY DIFFRACTIONr_scbond_it0.99937238
X-RAY DIFFRACTIONr_scangle_it1.6434.56278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2557tight positional0.050.05
2B2454tight positional0.020.05
3C2441tight positional0.040.05
4G580tight positional0.050.05
4G544medium positional0.250.5
1A2557tight thermal0.050.5
2B2454tight thermal0.490.5
3C2441tight thermal0.040.5
4G580tight thermal0.750.5
4G544medium thermal0.982
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 363 -
Rwork0.27 7073 -
obs--96.37 %
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)
10.8327-0.12160.58980.5566-0.05180.4199-0.04620.14720.1469-0.0024-0.0499-0.10720.00670.1280.096-0.0587-0.02570.0119-0.02170.0827-0.072511.32416.38-25.207
20.40260.1756-0.04770.9612-0.74080.78020.02190.0844-0.0083-0.07820.05630.13640.1115-0.0888-0.0783-0.0311-0.0098-0.0011-0.1026-0.02-0.161-9.242-10.302-31.024
30.83340.02960.24150.7506-0.38150.91820.03080.0656-0.01180.08020.05140.17840.0079-0.0101-0.0823-0.0913-0.06030.0409-0.1132-0.0096-0.0855-19.191-27.95-5.005
40.3797-0.3269-0.1990.6750.41090.2796-0.0774-0.03740.01060.06070.03180.03740.03130.05870.0456-0.0356-0.00690.0505-0.05890.0245-0.1466-13.229-15.08525.822
51.26690.3542-0.78120.6413-0.20870.92980.0782-0.16480.23840.11850.036-0.0445-0.14440.2061-0.1143-0.0404-0.0508-0.01350.0124-0.077-0.06097.55811.65231.851
61.05160.1106-0.45660.67840.17910.74670.0420.0040.27880.06890.03220.10820.020.0135-0.0742-0.0325-0.0752-0.0158-0.11130.01570.016922.07225.6745.606
73.171-0.689-1.01184.81110.32721.6333-0.0381-0.1257-0.30220.0751-0.14840.33440.0655-0.27490.1865-0.09750.05630.0077-0.0125-0.0340.0369-23.29221.569-19.596
85.5674-0.84350.6193.5978-0.6322.7953-0.13830.00820.5941-0.1032-0.0144-0.3201-0.27650.08990.1528-0.04450.0464-0.0465-0.10130.00690.0766-26.72317.11420.219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 3286 - 328
2X-RAY DIFFRACTION2BB21 - 32821 - 328
3X-RAY DIFFRACTION3CC22 - 32822 - 328
4X-RAY DIFFRACTION4DD6 - 3286 - 328
5X-RAY DIFFRACTION5EE21 - 32821 - 328
6X-RAY DIFFRACTION6FF22 - 32822 - 328
7X-RAY DIFFRACTION7GG115 - 2593 - 147
8X-RAY DIFFRACTION8HH115 - 2593 - 147

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