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- PDB-2vy3: Type IV secretion system effector protein BepA -

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Basic information

Entry
Database: PDB / ID: 2vy3
TitleType IV secretion system effector protein BepA
ComponentsCELL FILAMENTATION PROTEIN
KeywordsCELL ADHESION / T4SS / OB FOLD / FIC DOMAIN / SUBSTRATE PROTEIN / PROTEIN TRANSLOCATION
Function / homology
Function and homology information


AMPylase activity / protein adenylylation / protein adenylyltransferase / symbiont-mediated suppression of host apoptosis / regulation of cell division / extracellular region / ATP binding
Similarity search - Function
BepA, intracellular delivery domain / Intracellular delivery domain / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...BepA, intracellular delivery domain / Intracellular delivery domain / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Protein adenylyltransferase
Similarity search - Component
Biological speciesBARTONELLA HENSELAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsPalanivelu, D.V. / Schirmer, T.
CitationJournal: Protein Sci. / Year: 2011
Title: Fic Domain Catalyzed Adenylylation: Insight Provided by the Structural Analysis of the Type Iv Secretion System Effector Bepa.
Authors: Palanivelu, D.V. / Goepfert, A. / Meury, M. / Guye, P. / Dehio, C. / Schirmer, T.
History
DepositionJul 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _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: CELL FILAMENTATION PROTEIN
B: CELL FILAMENTATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0088
Polymers69,7022
Non-polymers3066
Water1267
1
A: CELL FILAMENTATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0044
Polymers34,8511
Non-polymers1533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELL FILAMENTATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0044
Polymers34,8511
Non-polymers1533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.336, 84.610, 126.680
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
12A
22B
13A
23B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEPROPROAA13 - 2213 - 22
211ILEILEPROPROBB13 - 2213 - 22
121THRTHRILEILEAA26 - 3326 - 33
221THRTHRILEILEBB26 - 3326 - 33
131LEULEUSERSERAA36 - 5836 - 58
231LEULEUSERSERBB36 - 5836 - 58
141TYRTYRALAALAAA62 - 10062 - 100
241TYRTYRALAALABB62 - 10062 - 100
151NINININIAC501
251NINININIBF501
171NINININIAD502
271NINININIBG502
112ARGARGGLUGLUAA125 - 142125 - 142
212ARGARGGLUGLUBB125 - 142125 - 142
122PHEPHELEULEUAA144 - 155144 - 155
222PHEPHELEULEUBB144 - 155144 - 155
132PROPROGLUGLUAA160 - 174160 - 174
232PROPROGLUGLUBB160 - 174160 - 174
142LEULEUARGARGAA176 - 238176 - 238
242LEULEUARGARGBB176 - 238176 - 238
113MSEMSEGLYGLYAA246 - 256246 - 256
213MSEMSEGLYGLYBB246 - 256246 - 256
123TYRTYRPROPROAA258 - 292258 - 292
223TYRTYRPROPROBB258 - 292258 - 292
133ILEILEALAALAAA296 - 300296 - 300
233ILEILEALAALABB296 - 300296 - 300

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.84351, -0.52903, -0.09279), (-0.52284, -0.84831, -0.0837), (-0.12299, 0.02208, -0.99216)49.687, 147.868, 136.036
2given(0.84676, -0.53007, -0.04504), (-0.52918, -0.84795, 0.03074), (-0.05448, -0.0022, -0.99851)47.464, 150.611, 134.693

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Components

#1: Protein CELL FILAMENTATION PROTEIN / BEPA PROTEIN / BEPA


Mass: 34851.102 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-302
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL (HIS)6-TAG WITH THROMBIN CLEAVAGE SITE / Source: (gene. exp.) BARTONELLA HENSELAE (bacteria) / Plasmid: PRUN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q6G2A9
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN BOTH CHAINS, RESIDUES 1 TO 11 ARE MISSING DUE TO DISORDER AND RESIDUES 303 TO 544 ARE MISSING ...IN BOTH CHAINS, RESIDUES 1 TO 11 ARE MISSING DUE TO DISORDER AND RESIDUES 303 TO 544 ARE MISSING DUE TO PROTEOLYTIC CLEAVAGE AND - OR DISORDER.

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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 % / Description: NONE
Crystal growpH: 8.7
Details: 17 MG/ML PROTEIN IN 20 MM TRIS-HCL (PH 8.0), 500 MM NACL AND 2 MM BETA-MERCAPTOETHANOL MIXED WITH 22 % POLYETHYLENE GLYCOL 4000, 0.1 M TRIS PH 8.7, 5 MM NICL2 IN A 1:1 (V:V) RATIO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97935
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.8→85.13 Å / Num. obs: 18356 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 5.56 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.25
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.37 / % possible all: 60.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 39.143 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 937 5.1 %RANDOM
Rwork0.216 ---
obs0.219 17372 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å2-0 Å2
2---0.82 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 6 7 4681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224545
X-RAY DIFFRACTIONr_bond_other_d0.0020.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.9466148
X-RAY DIFFRACTIONr_angle_other_deg0.82637419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2055567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9724.977221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03615734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9881518
X-RAY DIFFRACTIONr_chiral_restr0.0530.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02915
X-RAY DIFFRACTIONr_nbd_refined0.2140.2949
X-RAY DIFFRACTIONr_nbd_other0.1720.22976
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22229
X-RAY DIFFRACTIONr_nbtor_other0.0870.22357
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2161.53513
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43724549
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.64131873
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8274.51599
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1106tight positional0.180.05
12B1106tight positional0.180.05
21A1435tight positional0.130.05
22B1435tight positional0.130.05
31A603tight positional0.120.05
32B603tight positional0.120.05
11A1106tight thermal0.380.5
12B1106tight thermal0.380.5
21A1435tight thermal0.30.5
22B1435tight thermal0.30.5
31A603tight thermal0.230.5
32B603tight thermal0.230.5
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.364 88
Rwork0.342 1334
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)
11.5171.2866-1.10522.4019-1.3433.0791-0.1137-0.0326-0.0401-0.17740.0064-0.15810.20770.12130.1073-0.33160.0372-0.00950.005-0.0153-0.30710.62460.66349.253
23.18063.20343.0895.34831.54.2234-0.14840.18360.46820.25140.2203-0.6019-0.13640.6152-0.0719-0.2281-0.011-0.00950.3710.0396-0.247212.62558.99270.123
37.8260.73083.37673.441-0.41767.8208-0.0315-1.0577-0.10310.9662-0.1693-0.51410.40380.27310.20080.0754-0.0143-0.13370.5340.0296-0.14417.06158.67685.921
41.4444-1.31150.32384.9883-0.39565.14340.0683-0.1115-0.0172-0.3888-0.0390.135-0.59690.0415-0.0292-0.11460.036-0.0210.0579-0.0493-0.275422.03595.38684.937
50.43510.5308-0.76595.3193.10224.8883-0.01630.2118-0.2236-0.28560.0821-0.0309-1.15840.1514-0.06580.06370.0373-0.0720.07070.0395-0.252123.96795.45263.798
69.1853-4.4423-2.4022.9905-1.59039.62230.75311.734-0.4631-1.6681-0.7088-0.4557-0.8421-0.1842-0.04430.54180.0729-0.07840.6351-0.1456-0.234627.05594.02147.796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 180
2X-RAY DIFFRACTION1A501 - 601
3X-RAY DIFFRACTION2A181 - 244
4X-RAY DIFFRACTION3A245 - 302
5X-RAY DIFFRACTION4B13 - 180
6X-RAY DIFFRACTION4B501 - 601
7X-RAY DIFFRACTION5B181 - 244
8X-RAY DIFFRACTION6B245 - 302

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