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- PDB-2jk8: Type IV secretion system effector protein BepA complexed with a p... -

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Basic information

Entry
Database: PDB / ID: 2jk8
TitleType IV secretion system effector protein BepA complexed with a pyrophosphate moiety
ComponentsPUTATIVE CELL FILAMENTATION PROTEIN (BEPA PROTEIN)
KeywordsCELL ADHESION / T4SS / OB FOLD / FIC DOMAIN / SUBSTRATE PROTEIN / PROTEIN TRANSLOCATION
Function / homology
Function and homology information


AMPylase activity / protein adenylyltransferase / protein adenylylation / 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
ADENOSINE-5'-TRIPHOSPHATE / NICKEL (II) ION / Protein adenylyltransferase
Similarity search - Component
Biological speciesBARTONELLA HENSELAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
DepositionAug 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 2, 2011Group: Database references / Other / Refinement description
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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.pdbx_dist_value / _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: PUTATIVE CELL FILAMENTATION PROTEIN (BEPA PROTEIN)
B: PUTATIVE CELL FILAMENTATION PROTEIN (BEPA PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5669
Polymers68,7642
Non-polymers8027
Water1267
1
A: PUTATIVE CELL FILAMENTATION PROTEIN (BEPA PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0315
Polymers34,3821
Non-polymers6494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE CELL FILAMENTATION PROTEIN (BEPA PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5354
Polymers34,3821
Non-polymers1533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.948, 82.877, 126.729
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
251NINININIBG501
161HOHHOHHOHHOHAJ2001 - 2002
261HOHHOHHOHHOHBK2001 - 2002
171NINININIAD502
271NINININIBH502
181HOHHOHHOHHOHAJ2003
281HOHHOHHOHHOHBK2003
112ARGARGGLUGLUAA125 - 142125 - 142
212ARGARGGLUGLUBB125 - 142125 - 142
122PHEPHELEULEUAA144 - 155144 - 155
222PHEPHELEULEUBB144 - 155144 - 155
132PROPROGLUGLUAA160 - 174160 - 174
232PROPROGLUGLUBB160 - 174160 - 174
142LEULEUARGARGAA176 - 238176 - 238
242LEULEUARGARGBB176 - 238176 - 238
113METMETGLYGLYAA246 - 256246 - 256
213METMETGLYGLYBB246 - 256246 - 256
123TYRTYRPROPROAA258 - 292258 - 292
223TYRTYRPROPROBB258 - 292258 - 292
133ILEILEALAALAAA296 - 300296 - 300
233ILEILEALAALABB296 - 300296 - 300

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.86795, -0.49152, -0.0712), (-0.48379, -0.86915, 0.10261), (-0.11232, -0.05462, -0.99217)44.181, 145.429, 137.406
2given(0.86803, -0.49494, -0.03941), (-0.49375, -0.86884, 0.03652), (-0.05231, -0.01224, -0.99856)42.974, 148.572, 134.811

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PUTATIVE CELL FILAMENTATION PROTEIN (BEPA PROTEIN) / BEPA


Mass: 34382.156 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

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Non-polymers , 5 types, 14 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsADENOSINE-5'-TRIPHOSPHATE (ATP): ONLY TWO PHOSPHATES ARE VISIBLE IN THE DENSITY
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 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 8.7
Details: 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: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.73→82.76 Å / Num. obs: 17907 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.62 / % possible all: 55.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VY3

2vy3


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 33.897 / SU ML: 0.297 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 890 5 %RANDOM
Rwork0.216 ---
obs0.218 16976 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 15 7 4690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224556
X-RAY DIFFRACTIONr_bond_other_d0.0020.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9496161
X-RAY DIFFRACTIONr_angle_other_deg0.86737419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2375567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21924.977221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82415734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1021518
X-RAY DIFFRACTIONr_chiral_restr0.060.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02915
X-RAY DIFFRACTIONr_nbd_refined0.2120.2957
X-RAY DIFFRACTIONr_nbd_other0.1780.22899
X-RAY DIFFRACTIONr_nbtor_refined0.180.22203
X-RAY DIFFRACTIONr_nbtor_other0.090.22390
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9421.52902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50924549
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.71231820
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2794.51612
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 / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11106tight positional0.20.05
21435tight positional0.140.05
3603tight positional0.110.05
11106tight thermal0.440.5
21435tight thermal0.350.5
3603tight thermal0.190.5
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.409 56
Rwork0.308 1060
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)
11.91871.4178-1.48542.672-1.70313.9395-0.0495-0.1113-0.0754-0.0508-0.0820.02530.16460.2440.1315-0.22450.0103-0.0166-0.2483-0.0047-0.077411.25258.69249.117
23.0552.08372.5596.28451.08242.2340.1582-0.29920.26380.40880.0946-0.665-0.07650.6507-0.2528-0.0263-0.06380.09690.08730.02460.090513.07957.23270.225
39.674-0.73352.40026.8666-0.11134.8833-0.1276-1.00110.20161.01290.0148-0.1482-0.01310.59440.11270.2889-0.0257-0.13370.7292-0.00140.150717.41757.3486.359
42.2678-0.51890.58664.5769-0.21754.8670.1117-0.1234-0.0584-0.3135-0.06260.2906-0.2616-0.0578-0.0491-0.1330.01910.0143-0.2555-0.0145-0.080421.52594.29284.526
51.21810.267-0.18916.0943.69945.29640.23680.3518-0.0298-0.3076-0.0279-0.1221-0.79840.1711-0.20890.02810.0217-0.0696-0.15620.07690.005723.40994.36963.164
616.7805-2.45270.4668.007-0.980311.19920.62092.795-0.1949-1.9943-0.78690.1658-0.5049-0.01450.1660.5440.1625-0.0360.5483-0.01740.023126.47292.99747.247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 180
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION1A701 - 702
4X-RAY DIFFRACTION1A2001 - 2004
5X-RAY DIFFRACTION2A181 - 244
6X-RAY DIFFRACTION3A245 - 302
7X-RAY DIFFRACTION4B13 - 180
8X-RAY DIFFRACTION4B501 - 502
9X-RAY DIFFRACTION4B601
10X-RAY DIFFRACTION5B181 - 244
11X-RAY DIFFRACTION6B245 - 302

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