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- PDB-3zcj: Crystal structure of Helicobacter pylori T4SS protein CagL in a t... -

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Basic information

Entry
Database: PDB / ID: 3zcj
TitleCrystal structure of Helicobacter pylori T4SS protein CagL in a tetragonal crystal form with a helical RGD-motif (6 Mol per ASU)
ComponentsCAGL
KeywordsPROTEIN BINDING / ADHESION / RGD MOTIF / INTEGRIN BINDING / TYPE IV SECRETION / T4S / VIRULENCE / CAG18 / HP0539 / METHYLATED
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #1660 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Cag pathogenicity island protein (Cag18)
Function and homology information
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsBarden, S. / Niemann, H.H.
CitationJournal: Structure / Year: 2013
Title: A Helical Rgd Motif Promoting Cell Adhesion: Crystal Structures of the Helicobacter Pylori Type Iv Secretion System Pilus Protein Cagl
Authors: Barden, S. / Lange, S. / Tegtmeyer, N. / Conradi, J. / Sewald, N. / Backert, S. / Niemann, H.H.
History
DepositionNov 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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

Downloads & links

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Assembly

Deposited unit
A: CAGL
B: CAGL
C: CAGL
D: CAGL
E: CAGL
F: CAGL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,93018
Polymers152,8586
Non-polymers1,07212
Water1086
1
A: CAGL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7674
Polymers25,4761
Non-polymers2903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CAGL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7554
Polymers25,4761
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CAGL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5682
Polymers25,4761
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CAGL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6083
Polymers25,4761
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: CAGL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5682
Polymers25,4761
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: CAGL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6633
Polymers25,4761
Non-polymers1872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)197.122, 197.122, 106.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND RESID 20:52 AND (NAME O OR NAME CA OR NAME N OR NAME C))
211(CHAIN B AND RESID 20:52 AND (NAME O OR NAME CA OR NAME N OR NAME C))
311(CHAIN C AND RESID 20:52 AND (NAME O OR NAME CA OR NAME N OR NAME C))
411(CHAIN D AND RESID 20:52 AND (NAME O OR NAME CA OR NAME N OR NAME C))
511(CHAIN F AND RESID 20:52 AND (NAME O OR NAME CA OR NAME N OR NAME C))
611(CHAIN E AND RESID 20:52 AND (NAME O OR NAME CA OR NAME N OR NAME C))

NCS oper:
IDCodeMatrixVector
1given(-0.98421, -0.02088, -0.17576), (0.02161, 0.97141, -0.23642), (0.17568, -0.23649, -0.95562)-11.38522, 11.31287, 25.02733
2given(0.34404, 0.83057, -0.43794), (0.64963, 0.12621, 0.7497), (0.67796, -0.54243, -0.49614)51.79665, -56.19586, -21.13411
3given(-0.39723, 0.91254, 0.0974), (-0.45275, -0.10255, -0.88572), (-0.79826, -0.39593, 0.45389)47.44381, -44.06326, -46.81049
4given(-0.16368, 0.45246, -0.87663), (-0.91019, 0.27345, 0.31109), (0.38047, 0.84883, 0.36707)54.87707, -67.51531, 56.26179
5given(0.37936, 0.61967, 0.68709), (0.82412, 0.11128, -0.55538), (-0.42061, 0.77694, -0.46846)31.9315, -47.91024, 54.92276

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
CAGL


Mass: 25476.318 Da / Num. of mol.: 6 / Fragment: RESIDUES 21-237
Source method: isolated from a genetically manipulated source
Details: PRIMARY AMINES (N-TERMINUS AND LYSINES) REDUCTIVELY METHYLATED
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: O25272

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Non-polymers , 5 types, 18 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPOTASSIUM ION (K): CRYSTALLIZATION COCKTAIL COMPOUND PHOSPHATE ION (PO4): CRYSTALLIZATION COCKTAIL ...POTASSIUM ION (K): CRYSTALLIZATION COCKTAIL COMPOUND PHOSPHATE ION (PO4): CRYSTALLIZATION COCKTAIL COMPOUND GLYCEROL (GOL): CRYO PROTECTANT N-DIMETHYL-LYSINE (MLY): REDUCTIVELY METHYLATED LYSINES FACILITATING CRYSTALLIZATION DI(HYDROXYETHYL)ETHER (PEG): CRYSTALLIZATION COCKTAIL COMPOUND

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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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: PROTEIN CONCENTRATION: 10 MG/ML. RESERVOIR: 22.5% PEG 3350, 200 MM KCL. VAPOR DIFFUSION AT 277 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.25→58.34 Å / Num. obs: 33724 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 69.97 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 8.1
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZCI

3zci


Resolution: 3.25→55.965 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 24.41 / Stereochemistry target values: ML
Details: RESTRAINED TO REFERENCE STRUCTURE AND SECONDARY STRUCTURE RESTRAINTS APPLIED
RfactorNum. reflection% reflection
Rfree0.2513 1706 5.1 %
Rwork0.2051 --
obs0.2075 33663 99.96 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.671 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 91.08 Å2
Baniso -1Baniso -2Baniso -3
1-4.8458 Å20 Å20 Å2
2--4.8458 Å20 Å2
3----9.6915 Å2
Refinement stepCycle: LAST / Resolution: 3.25→55.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9370 0 66 6 9442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069512
X-RAY DIFFRACTIONf_angle_d0.92912770
X-RAY DIFFRACTIONf_dihedral_angle_d15.2223712
X-RAY DIFFRACTIONf_chiral_restr0.0531451
X-RAY DIFFRACTIONf_plane_restr0.0051578
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A116X-RAY DIFFRACTIONPOSITIONAL
12B116X-RAY DIFFRACTIONPOSITIONAL0.145
13C104X-RAY DIFFRACTIONPOSITIONAL0.164
14D108X-RAY DIFFRACTIONPOSITIONAL0.203
15F108X-RAY DIFFRACTIONPOSITIONAL0.19
16E96X-RAY DIFFRACTIONPOSITIONAL0.178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2501-3.34570.35251380.28722632X-RAY DIFFRACTION100
3.3457-3.45370.28711330.25372614X-RAY DIFFRACTION100
3.4537-3.57710.28281410.23212609X-RAY DIFFRACTION100
3.5771-3.72030.25711320.22622632X-RAY DIFFRACTION100
3.7203-3.88960.24391470.2072616X-RAY DIFFRACTION100
3.8896-4.09460.29921340.19212657X-RAY DIFFRACTION100
4.0946-4.3510.23891380.17382625X-RAY DIFFRACTION100
4.351-4.68680.20621640.16582645X-RAY DIFFRACTION100
4.6868-5.15810.23181530.1652654X-RAY DIFFRACTION100
5.1581-5.90380.31281530.23592679X-RAY DIFFRACTION100
5.9038-7.43550.31021310.24172723X-RAY DIFFRACTION100
7.4355-55.97330.19971420.19232871X-RAY DIFFRACTION100
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)
18.2293-1.3376-0.22724.435-0.41216.55960.1535-0.23340.06920.0663-0.28780.27620.9449-0.34540.05510.3014-0.0755-0.02670.21450.15480.26184.5143-36.631825.6826
25.87371.87633.13826.59841.65877.30930.0887-0.41290.30290.5041-0.2501-0.3156-0.08170.1557-0.27280.307-0.1290.00160.1345-0.10040.323720.4132-22.151435.4208
32.3780.80480.52590.59690.33961.9581-0.13670.58220.6026-0.34590.26630.4219-0.2663-0.2660.65360.2359-0.1707-0.16590.40550.37410.21-8.1556-24.4024-1.8087
41.1458-0.5935-1.00774.9709-0.6831.7062-0.0146-0.2261-0.09450.7585-0.0528-0.4482-0.06160.60160.02050.0745-0.0465-0.04110.1516-0.04120.197817.7215-34.9324.9853
51.7108-0.93490.69282.2586-0.72562.60350.13220.77080.1272-0.8135-0.10010.32510.2876-0.3339-0.11240.2767-0.1066-0.00350.5130.19030.1105-3.3027-33.6691-6.5633
68.3096-1.88653.42927.7061-2.43619.81710.2371.3099-0.3153-1.16460.11720.09410.52751.4523-0.23420.291-0.099-0.03980.35680.04710.4309-17.3013-46.78726.2824
73.98170.13891.40722.0193-0.13261.9095-0.04650.4118-0.2105-0.320.03420.33150.01670.0447-0.33860.1299-0.1601-0.16790.10180.15630.2888-24.6561-35.957-0.2443
82.2117-0.30971.08690.8314-0.16171.6610.069-0.75910.58540.3526-0.0979-0.0786-0.2898-0.0640.36380.4885-0.4556-0.16590.5532-0.05310.2918-8.7751-27.926435.278
91.31151.7432-0.66473.8961-0.83881.16590.00330.1416-0.0891-0.25420.1497-0.03010.4596-0.2817-0.18540.2755-0.1308-0.13460.15790.14370.2339-30.077-48.01833.9627
104.42510.69872.0552.39461.1922.47320.322-1.52620.42040.7991-0.4239-0.230.4442-0.4784-0.37370.381-0.4322-0.06430.72850.14230.4811-14.8013-37.111637.552
112.97472.191.01088.96661.64995.63160.16490.7746-1.2612-0.4094-0.56210.01381.20040.46110.30580.80770.3708-0.03330.78710.05970.476126.84-62.593912.5243
126.07353.2274-1.93113.8388-1.45831.0502-0.12860.9252-0.5207-0.44440.0375-0.77240.29240.5413-0.32270.24240.1255-0.09090.89220.00410.356840.8658-55.61116.3447
131.3135-0.81420.07173.99980.53720.1023-0.1155-0.9871-0.2440.8861-0.08720.84040.2521-0.4036-0.05770.2572-0.20310.09030.8650.12570.3218.9627-57.250642.6692
141.5356-1.32110.08752.44911.15777.03140.31450.5619-0.0055-0.4659-0.0962-0.2973-0.31120.9504-0.11490.19020.0842-0.17680.32820.06670.176725.6015-51.145716.0972
153.9242-1.4043-3.53190.50271.26423.17910.3246-1.04730.39450.6499-0.04440.5742-0.6311-0.1393-0.56550.41410.13220.26381.0060.02330.6485-2.3449-49.86942.419
165.36-1.71810.26987.4016-0.65344.4991-0.6803-1.1783-0.7770.6889-0.1002-0.08320.5463-0.10110.26960.8474-0.154-0.03890.41020.2160.4127-43.6509-68.928421.9627
173.7175-1.7520.52722.9769-0.02532.71940.014-0.3036-0.3087-0.15270.0336-0.10560.0688-0.2005-0.21780.2645-0.2405-0.21710.359-0.08530.3552-42.9156-67.402210.2752
182.1008-2.1034-0.61022.11710.88573.22180.23461.5742-0.778-1.1248-0.3539-1.19030.26851.04780.2440.54090.03810.3461.1036-0.11991.0817-16.6108-71.2355-8.703
191.8443-0.3007-3.63931.78241.92498.1880.14170.22190.2830.0931-0.12070.1399-0.1126-0.7163-0.00580.3761-0.1479-0.20310.31140.14190.2732-40.2861-58.964316.112
202.77051.2099-1.74210.5878-0.59211.56520.6890.75270.9833-1.4196-0.1268-2.328-0.96151.7101-0.71280.9896-0.16180.37211.5831-0.04741.7103-6.3139-64.6102-2.6623
213.9373-0.56090.97871.4238-1.12954.72140.0582-0.02790.73452.1748-0.3975-0.7210.2170.32110.20310.6204-0.3713-0.14381.0494-0.10570.6098-31.2362-41.176642.6079
222.90270.4814-0.89352.8493-1.12872.13860.3836-0.51760.28120.4357-0.3165-0.02080.26520.209-0.14140.6598-0.14210.11670.55010.01150.0626-44.1303-53.946146.5464
234.6113-1.1375-0.74057.30080.40622.50810.06620.0949-0.45930.43620.41952.57960.0482-1.9909-0.86211.0946-0.12970.01651.13280.42391.1177-62.9858-78.163851.5461
244.35353.0863-1.78496.7522-2.32862.71180.02180.21361.00550.12140.44881.3177-0.0689-0.593-0.55320.2803-0.0785-0.01140.51220.05350.3156-45.064-50.380237.4876
252.68372.4496-1.05486.7356-0.82852.9145-0.20390.1581-0.3386-0.14740.4136-0.1360.8735-0.1862-0.00490.8225-0.21360.06480.78270.00920.1811-44.7493-69.309138.3966
268.6198-3.006-0.04939.0489-3.88152.48110.03721.0228-0.2075-1.22760.40670.6529-0.0792-1.5667-0.38850.62460.0374-0.01261.032-0.08360.289510.8821-38.5194-11.5849
272.201-0.07220.39341.89440.88794.08880.25780.4204-0.4564-0.0441-0.1907-0.05490.88170.0770.03120.54650.07540.15820.6221-0.11770.108921.2678-47.8478-14.1843
281.5961-0.0451-0.73330.63490.57960.8291-0.44590.2675-0.756-0.8249-0.22540.70120.52420.0038-0.37372.06660.40990.18730.8621-0.25420.90729.01-76.5705-15.674
294.5437-2.8839-1.05916.06610.83812.60960.36460.59890.2084-0.958-0.1954-0.83480.07680.627-0.01810.3816-0.13310.00790.74340.03030.172424.8879-43.0693-6.7319
303.0312-1.8010.99672.7012-1.76361.58-0.11320.2228-0.6197-0.13640.33620.11940.39460.2468-0.12520.40890.05530.05610.5412-0.06680.302221.4083-58.1556-3.1765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 21:51)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 58:78)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 79:163)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 164:190)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 191:231)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 23:52)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 58:90)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 91:167)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 168:189)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 190:229)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 23:47)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 48:90)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 91:156)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 157:210)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 211:226)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 23:48)
17X-RAY DIFFRACTION17(CHAIN D AND RESID 60:106)
18X-RAY DIFFRACTION18(CHAIN D AND RESID 107:156)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 157:210)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 211:227)
21X-RAY DIFFRACTION21(CHAIN F AND RESID 22:65)
22X-RAY DIFFRACTION22(CHAIN F AND RESID 66:116)
23X-RAY DIFFRACTION23(CHAIN F AND RESID 117:135)
24X-RAY DIFFRACTION24(CHAIN F AND RESID 136:189)
25X-RAY DIFFRACTION25(CHAIN F AND RESID 190:230)
26X-RAY DIFFRACTION26(CHAIN E AND RESID 25:47)
27X-RAY DIFFRACTION27(CHAIN E AND RESID 48:108)
28X-RAY DIFFRACTION28(CHAIN E AND RESID 109:145)
29X-RAY DIFFRACTION29(CHAIN E AND RESID 146:184)
30X-RAY DIFFRACTION30(CHAIN E AND RESID 185:224)

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