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- PDB-2bhv: Structure of ComB10 of the Com Type IV secretion system of Helico... -

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Basic information

Entry
Database: PDB / ID: 2bhv
TitleStructure of ComB10 of the Com Type IV secretion system of Helicobacter pylori
ComponentsCOMB10
KeywordsBACTERIAL PROTEIN / BACTERIAL TYPE IV SECRETION
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #160 / Type IV secretion system, VirB10/TraB/TrbI / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Lipocalin / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsTerradot, L. / Oomen, C. / Bayliss, R. / Leonard, G. / Waksman, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structures of Two Core Subunits of the Bacterial Type Iv Secretion System, Virb8 from Brucella Suis and Comb10 from Helicobacter Pylori
Authors: Terradot, L. / Bayliss, R. / Oomen, C. / Leonard, G. / Baron, C. / Waksman, G.
History
DepositionJan 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMB10
B: COMB10
C: COMB10
D: COMB10
E: COMB10
F: COMB10


Theoretical massNumber of molelcules
Total (without water)163,1016
Polymers163,1016
Non-polymers00
Water0
1
A: COMB10
E: COMB10


Theoretical massNumber of molelcules
Total (without water)54,3672
Polymers54,3672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-20.4 kcal/mol
Surface area19900 Å2
MethodPISA
2
B: COMB10
C: COMB10


Theoretical massNumber of molelcules
Total (without water)54,3672
Polymers54,3672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-21.2 kcal/mol
Surface area19870 Å2
MethodPISA
3
D: COMB10
F: COMB10


Theoretical massNumber of molelcules
Total (without water)54,3672
Polymers54,3672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-22.2 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.735, 139.411, 168.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A167 - 224
2111B167 - 224
3111C167 - 224
4111D167 - 224
5111E167 - 224
6111F167 - 224
1216A225 - 231
2216B225 - 231
3216C225 - 231
4216D225 - 231
5216E225 - 231
6216F225 - 231
1311A232 - 253
2311B232 - 253
3311C232 - 253
4311D232 - 253
5311E232 - 253
6311F232 - 253
1411A278 - 293
2411B278 - 293
3411C278 - 293
4411D278 - 293
5411E278 - 293
6411F278 - 293
1516A294 - 343
2516B294 - 343
3516C294 - 343
4516D294 - 343
5516E294 - 343
6516F294 - 343
1611A344 - 376
2611B344 - 376
3611C344 - 376
4611D344 - 376
5611E344 - 376
6611F344 - 376
1716A262 - 277
2716B262 - 277
3716C262 - 277
4716D262 - 277
5716E262 - 277
6716F262 - 277

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Components

#1: Protein
COMB10


Mass: 27183.570 Da / Num. of mol.: 6 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 131-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PPROEXHTC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O24883
Sequence detailsPYLORIGEN DATABASE

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 6
Details: 8-14% (W/V) POLYETHYLENE GLYCOL (PEG) 8000, 100MM SODIUM CACODYLATE PH6.0 AND 200 MM MAGNESIUM ACETATE, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 32829 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: OTHER / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.874 / SU ML: 0.416 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.476
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1671 5.1 %RANDOM
Rwork0.257 ---
obs0.259 31301 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---3.92 Å20 Å2
3---2.74 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8759 0 0 0 8759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228894
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.97612032
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30851120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85123.884345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.276151598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.251560
X-RAY DIFFRACTIONr_chiral_restr0.0830.21443
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.23593
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25960
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.2273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4081.55740
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70929131
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.72133447
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1774.52901
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

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A963tight positional0.040.05
2B963tight positional0.040.05
3C963tight positional0.040.05
4D963tight positional0.030.05
5E963tight positional0.030.05
6F963tight positional0.030.05
1A422loose positional2.655
2B422loose positional2.175
3C422loose positional3.185
4D422loose positional2.045
5E422loose positional1.865
6F422loose positional2.155
1A963tight thermal0.060.5
2B963tight thermal0.060.5
3C963tight thermal0.060.5
4D963tight thermal0.050.5
5E963tight thermal0.050.5
6F963tight thermal0.050.5
1A422loose thermal2.2710
2B422loose thermal2.8510
3C422loose thermal1.7910
4D422loose thermal2.5310
5E422loose thermal3.8210
6F422loose thermal2.8410
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 125
Rwork0.33 2223
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)
11.84930.7938-0.43375.03660.94732.54240.07280.19610.02780.0118-0.13230.6565-0.4871-0.2220.05950.21810.07760.02140.104-0.0041-0.0662-61.823-14.438-18.912
20.07270.4701-0.39073.0941-2.93955.3269-0.0304-0.02560.042-0.0734-0.467-0.6758-0.00570.8540.49740.1077-0.08580.00930.24460.05590.1131-28.932-27.15-25.729
30.04950.36770.55363.89975.07236.9801-0.04990.01830.1506-0.65430.3301-0.5239-0.85740.5009-0.28020.3075-0.01460.07080.1205-0.1080.01860.3294.95615.043
41.63051.08591.46532.09592.05512.9160.2294-0.2373-0.38790.138-0.38610.22150.1019-0.64530.15670.28890.1381-0.05460.3951-0.16010.1893-17.34631.49637.147
50.7273-2.647-0.55349.63382.0140.42110.2990.07660.3565-2.028-0.3693-1.0839-0.30670.44290.07021.13530.17670.16120.2390.05260.2553-4.82943.4636.016
62.1519-1.45431.29793.0017-1.00871.19050.0966-0.1923-0.4230.19970.04721.1507-0.0174-0.4866-0.14380.3166-0.0060.09080.3309-0.12670.3692-22.665-16.53428.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A166 - 376
2X-RAY DIFFRACTION2B165 - 376
3X-RAY DIFFRACTION3C166 - 376
4X-RAY DIFFRACTION4D166 - 376
5X-RAY DIFFRACTION5E166 - 376
6X-RAY DIFFRACTION6F166 - 376

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