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- PDB-3nts: Catalytic domain of VsdC from Aeromonas hydrophila -

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Basic information

Entry
Database: PDB / ID: 3nts
TitleCatalytic domain of VsdC from Aeromonas hydrophila
ComponentsVsdC
KeywordsTRANSFERASE / mono-ADP ribosyltransferase toxin
Function / homologyToxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / extracellular region / Alpha Beta / VsdC
Function and homology information
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsPfoh, R. / Shniffer, A. / Merrill, A.R. / Pai, E.F.
CitationJournal: To be Published
Title: Biochemical characterization of an actin-targeting ADP ribosyltransferase from aeromonas hydrophila and the identification of a novel inhibitor for this toxin family
Authors: Shniffer, A. / Suarez, G. / Turgeon, Z.J. / Pfoh, R. / Fieldhouse, R.J. / K Chopra, A. / Pai, E.F. / Merrill, A.R.
History
DepositionJul 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: VsdC
B: VsdC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4063
Polymers53,3102
Non-polymers961
Water00
1
A: VsdC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7512
Polymers26,6551
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VsdC


Theoretical massNumber of molelcules
Total (without water)26,6551
Polymers26,6551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.800, 87.800, 295.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22A
13B
23A
14B
24A
15B
25A
16B
26A
17B
27A
18B
28A
19B
29A
110B
210A
111B
211A
112B
212A
113B
213A
114B
214A
115B
215A
116B
216A
117B
217A
118B
218A
119B
219A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B68 - 80
2114A68 - 80
1121B81 - 90
2121A81 - 90
1134B91 - 116
2134A91 - 116
1141B117 - 120
2141A117 - 120
1154B121 - 144
2154A121 - 144
1161B151 - 166
2161A151 - 166
1174B167 - 172
2174A167 - 172
1181B173 - 182
2181A173 - 182
1194B183 - 187
2194A183 - 187
11101B188 - 192
21101A188 - 192
11114B193 - 195
21114A193 - 195
11121B196 - 206
21121A196 - 206
11131B207 - 220
21131A207 - 220
11144B221 - 229
21144A221 - 229
11151B230 - 246
21151A230 - 246
11164B247 - 248
21164A247 - 248
11171B249 - 263
21171A249 - 263
11184B264 - 266
21184A264 - 266
11196B145 - 150
21196A145 - 150

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19

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Components

#1: Protein VsdC


Mass: 26655.068 Da / Num. of mol.: 2 / Fragment: UNP residues 49-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: vsdC / Production host: Escherichia coli (E. coli) / References: UniProt: Q49TP5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 0.2 M sodium acetate, 5% glycerol, pH 7.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 4, 2010
RadiationMonochromator: multi-layer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.32→50 Å / Num. all: 10513 / Num. obs: 10417 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Rmerge(I) obs: 0.253 / Rsym value: 0.127
Reflection shellResolution: 3.32→3.42 Å / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / SU B: 94.962 / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.291 468 4.8 %RANDOM
Rwork0.2705 ---
all0.2715 9728 --
obs0.2715 9728 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 101.19 Å2 / Biso mean: 71.065 Å2 / Biso min: 21.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å21.36 Å20 Å2
2--2.73 Å20 Å2
3----4.09 Å2
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 5 0 2854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222901
X-RAY DIFFRACTIONr_angle_refined_deg0.8751.9953942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6535368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94124.05121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83615473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9991520
X-RAY DIFFRACTIONr_chiral_restr0.0560.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212180
X-RAY DIFFRACTIONr_mcbond_it0.2671.51862
X-RAY DIFFRACTIONr_mcangle_it0.48822978
X-RAY DIFFRACTIONr_scbond_it0.3331039
X-RAY DIFFRACTIONr_scangle_it0.6234.5964
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1101MEDIUM POSITIONAL0.410.5
1101MEDIUM THERMAL0.132
286TIGHT POSITIONAL0.010.05
286TIGHT THERMAL0.010.5
3193MEDIUM POSITIONAL0.250.5
3193MEDIUM THERMAL0.122
432TIGHT POSITIONAL0.010.05
432TIGHT THERMAL0.020.5
5164MEDIUM POSITIONAL0.230.5
5164MEDIUM THERMAL0.162
6121TIGHT POSITIONAL0.010.05
6121TIGHT THERMAL0.010.5
741MEDIUM POSITIONAL0.150.5
741MEDIUM THERMAL0.12
873TIGHT POSITIONAL0.020.05
873TIGHT THERMAL0.020.5
943MEDIUM POSITIONAL0.30.5
943MEDIUM THERMAL0.122
1040TIGHT POSITIONAL0.010.05
1040TIGHT THERMAL0.010.5
1127MEDIUM POSITIONAL0.110.5
1127MEDIUM THERMAL0.062
1273TIGHT POSITIONAL0.020.05
1273TIGHT THERMAL0.010.5
1360TIGHT POSITIONAL0.020.05
1360TIGHT THERMAL0.020.5
1479MEDIUM POSITIONAL0.70.5
1479MEDIUM THERMAL0.182
15123TIGHT POSITIONAL0.010.05
15123TIGHT THERMAL0.010.5
166MEDIUM POSITIONAL0.060.5
166MEDIUM THERMAL0.072
1765TIGHT POSITIONAL0.010.05
1765TIGHT THERMAL0.010.5
1822MEDIUM POSITIONAL0.120.5
1822MEDIUM THERMAL0.132
1947LOOSE POSITIONAL0.195
1947LOOSE THERMAL0.3210
LS refinement shellResolution: 3.4→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 29 -
Rwork0.388 654 -
all-683 -
obs--98.84 %
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)
11.0057-1.3808-0.65684.64272.94263.0913-0.2338-0.26150.32870.50130.3453-0.54740.48970.6504-0.11140.29090.2285-0.03870.32140.02960.2681-10.9603-32.9766-23.5226
22.7625-2.05420.93635.21950.30061.8454-0.05080.4249-0.32210.0652-0.19560.13060.1488-0.30150.24650.26750.10690.11890.3761-0.14510.2043-35.8475-28.0217-39.4017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A68 - 266
2X-RAY DIFFRACTION2B68 - 266

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