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- PDB-3tg2: Crystal structure of the ISC domain of VibB in complex with isoch... -

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Basic information

Entry
Database: PDB / ID: 3tg2
TitleCrystal structure of the ISC domain of VibB in complex with isochorismate
ComponentsVibriobactin-specific isochorismatase
KeywordsHYDROLASE / isochorismatase
Function / homology
Function and homology information


vibriobactin biosynthetic process / isochorismatase / isochorismatase activity
Similarity search - Function
Isochorismatase / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Rossmann fold ...Isochorismatase / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ISC / TRIETHYLENE GLYCOL / Vibriobactin-specific isochorismatase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.101 Å
AuthorsLiu, S. / Zhang, C. / Niu, B. / Li, N. / Liu, X. / Liu, M. / Wei, T. / Zhu, D. / Huang, Y. / Xu, S. / Gu, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction
Authors: Liu, S. / Zhang, C. / Li, N. / Niu, B. / Liu, M. / Liu, X. / Wei, T. / Zhu, D. / Huang, Y. / Xu, S. / Gu, L.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Nov 1, 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_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

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Assembly

Deposited unit
A: Vibriobactin-specific isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2153
Polymers24,8381
Non-polymers3762
Water4,774265
1
A: Vibriobactin-specific isochorismatase
hetero molecules

A: Vibriobactin-specific isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4296
Polymers49,6772
Non-polymers7534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area3830 Å2
ΔGint-7 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.584, 55.584, 119.792
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

#1: Protein Vibriobactin-specific isochorismatase / 2 / 3 dihydro-2 / 3 dihydroxybenzoate synthase / Isochorismate lyase-ArCP


Mass: 24838.283 Da / Num. of mol.: 1 / Fragment: ISC domain, UNP residues 1-215 / Mutation: D35N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: El Tor Inaba N16961 / Gene: VC_0771, vibB / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C6D3, isochorismatase
#2: Chemical ChemComp-ISC / (5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid / ISOCHORISMIC ACID


Mass: 226.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O6
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM CaCl2, 0.1M Bis-Tris pH 6.5, 28% PEG MME 500, 40mM MgCl2, 2.4mM chorismate, 0.02mg/ml EntC (isochrismate synthase from Escherichia coli O157) , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 87374 / Num. obs: 87374 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 44
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.528 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TB4

3tb4


Resolution: 1.101→25.21 Å / SU ML: 0.09 / σ(F): 0 / Phase error: 12.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1444 1923 2.29 %
Rwork0.1272 --
obs0.1276 83936 95.79 %
all-83936 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.628 Å2 / ksol: 0.432 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3644 Å20 Å20 Å2
2--0.3644 Å20 Å2
3----0.7288 Å2
Refinement stepCycle: LAST / Resolution: 1.101→25.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 26 265 1895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091790
X-RAY DIFFRACTIONf_angle_d1.4122472
X-RAY DIFFRACTIONf_dihedral_angle_d19.488708
X-RAY DIFFRACTIONf_chiral_restr0.08279
X-RAY DIFFRACTIONf_plane_restr0.008320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1007-1.12820.24931150.1987510684
1.1282-1.15870.171300.1465551691
1.1587-1.19280.1521330.1261554793
1.1928-1.23130.11861260.1076567894
1.2313-1.27530.14481350.1056574095
1.2753-1.32630.1151300.1056580695
1.3263-1.38670.12721350.1058584497
1.3867-1.45980.12051420.1058593997
1.4598-1.55130.12411440.1064597098
1.5513-1.6710.12471440.1088604099
1.671-1.83910.13891430.1153604199
1.8391-2.10510.13421470.1169613699
2.1051-2.65180.13181490.12556216100
2.6518-25.21690.1691500.14896434100

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