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- PDB-3n3u: Crystal Structure of IbpAFic2 -

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Basic information

Entry
Database: PDB / ID: 3n3u
TitleCrystal Structure of IbpAFic2
ComponentsAdenosine monophosphate-protein transferase ibpA
KeywordsTRANSFERASE / Fic domain
Function / homology
Function and homology information


AMPylase activity / protein adenylyltransferase / protein adenylylation / negative regulation of GTPase activity / cell outer membrane / protein modification process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis / extracellular region / ATP binding
Similarity search - Function
Peptidase C58, Yersinia/Haemophilus virulence surface antigen / Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Fido domain-containing protein / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Hemagglutinin repeat / Hemagglutinin repeat / ESPR domain ...Peptidase C58, Yersinia/Haemophilus virulence surface antigen / Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Fido domain-containing protein / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Hemagglutinin repeat / Hemagglutinin repeat / ESPR domain / Extended Signal Peptide of Type V secretion system / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein adenylyltransferase and cysteine protease IbpA
Similarity search - Component
Biological speciesHistophilus somni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.846 Å
AuthorsXiao, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis of Fic-mediated adenylylation.
Authors: Xiao, J. / Worby, C.A. / Mattoo, S. / Sankaran, B. / Dixon, J.E.
History
DepositionMay 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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_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_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: Adenosine monophosphate-protein transferase ibpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7974
Polymers33,5701
Non-polymers2273
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.380, 64.380, 149.689
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-161-

HOH

21A-175-

HOH

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Components

#1: Protein Adenosine monophosphate-protein transferase ibpA / AMPylator ibpA


Mass: 33569.922 Da / Num. of mol.: 1 / Fragment: Fido 2 domain residues 3488-3786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Histophilus somni (bacteria) / Strain: 2336 / Gene: HSM_1489, ibpA, p76 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q06277, nicotinamide-nucleotide adenylyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 550 MME, MES, ZnSO4, pH 6.5, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.2.121.2824
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 30, 2009
ADSC QUANTUM 315r2CCDJun 30, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28241
ReflectionRedundancy: 10.3 % / Av σ(I) over netI: 52.04 / Number: 257894 / Rmerge(I) obs: 0.061 / Χ2: 2.12 / D res high: 2 Å / D res low: 50 Å / Num. obs: 24925 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.435098.410.055.5439.4
4.315.4399.910.0494.1799.9
3.764.3110010.0513.6319.7
3.423.7610010.0583.7469.7
3.173.4210010.0633.4810
2.993.1710010.0662.98910.2
2.842.9910010.0692.60810.3
2.712.8410010.0782.24210.5
2.612.7110010.0811.82810.5
2.522.6110010.0931.6910.6
2.442.5210010.1021.48210.6
2.372.4410010.1121.31110.6
2.312.3710010.121.20910.7
2.252.3110010.1361.13810.6
2.22.2510010.1551.09810.6
2.152.210010.181.01710.7
2.112.1510010.2360.96410.6
2.072.1110010.280.89810.7
2.032.0710010.30.91310.6
22.0310010.3550.83310.6
ReflectionResolution: 1.85→50 Å / Num. obs: 31631 / % possible obs: 99.7 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.044 / Χ2: 1.026 / Net I/σ(I): 14.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 9 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3 / Num. unique all: 1527 / Χ2: 0.654 / % possible all: 98.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.846→31.471 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.814 / SU ML: 0.26 / σ(F): 1.33 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1592 5.04 %
Rwork0.212 --
obs0.213 31559 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.234 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 181.93 Å2 / Biso mean: 50.909 Å2 / Biso min: 17.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.722 Å2-0 Å20 Å2
2---2.722 Å2-0 Å2
3---5.443 Å2
Refinement stepCycle: LAST / Resolution: 1.846→31.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 7 204 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032329
X-RAY DIFFRACTIONf_angle_d0.6823141
X-RAY DIFFRACTIONf_chiral_restr0.049363
X-RAY DIFFRACTIONf_plane_restr0.002410
X-RAY DIFFRACTIONf_dihedral_angle_d16.009895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.846-1.9060.3181440.2722618276297
1.906-1.9740.2911340.25826672801100
1.974-2.0530.3241400.24427102850100
2.053-2.1460.3191580.24827022860100
2.146-2.260.2281490.22626572806100
2.26-2.4010.2341360.22427372873100
2.401-2.5860.2541480.23227172865100
2.586-2.8460.2581560.22727082864100
2.846-3.2580.281510.22127482899100
3.258-4.1030.2161380.18427812919100
4.103-31.4750.1921380.1842922306099
Refinement TLS params.Method: refined / Origin x: 29.6888 Å / Origin y: -12.8019 Å / Origin z: -11.5092 Å
111213212223313233
T0.3213 Å20.1779 Å20.0421 Å2-0.239 Å20.0037 Å2--0.1191 Å2
L1.8205 °2-1.0125 °2-0.1497 °2-2.388 °20.2542 °2--1.8501 °2
S-0.4231 Å °-0.379 Å °-0.0764 Å °0.413 Å °0.4947 Å °0.1344 Å °0.1251 Å °0.2029 Å °-0.0535 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3488 - 402
2X-RAY DIFFRACTION1allA1
3X-RAY DIFFRACTION1allA1 - 204

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