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- PDB-3tb4: Crystal structure of the ISC domain of VibB -

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Basic information

Entry
Database: PDB / ID: 3tb4
TitleCrystal structure of the ISC domain of VibB
ComponentsVibriobactin-specific isochorismatase
KeywordsHYDROLASE / ISC domain / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Vibriobactin-specific isochorismatase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLiu, S. / Zhang, C. / Niu, B. / Li, N. / Liu, M. / Wei, T. / Zhu, D. / 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 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,4906
Polymers24,8391
Non-polymers6515
Water5,044280
1
A: Vibriobactin-specific isochorismatase
hetero molecules

A: Vibriobactin-specific isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,98012
Polymers49,6792
Non-polymers1,30210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area5120 Å2
ΔGint-28 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.657, 55.657, 118.746
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-675-

HOH

21A-762-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 24839.268 Da / Num. of mol.: 1 / Fragment: ISC domain, UNP residues 1-215
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: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 284 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 550MME, 0.1M Bis-Tris pH 6.5, 50mM CaCl2, 1% B-OCTYLGLUCOSIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 18, 2010
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 47657 / Num. obs: 47657 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 13.78 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 45.8
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.486 / % possible all: 100

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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 2FQ1

2fq1


Resolution: 1.35→22.765 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1662 1929 4.23 %RANDOM
Rwork0.1342 ---
obs0.1355 45613 95.76 %-
all-45613 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.239 Å2 / ksol: 0.419 e/Å3
Displacement parametersBiso mean: 19.7165 Å2
Baniso -1Baniso -2Baniso -3
1-0.2111 Å20 Å2-0 Å2
2--0.2111 Å2-0 Å2
3----0.4221 Å2
Refinement stepCycle: LAST / Resolution: 1.35→22.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 42 280 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011776
X-RAY DIFFRACTIONf_angle_d1.3172435
X-RAY DIFFRACTIONf_dihedral_angle_d16.793690
X-RAY DIFFRACTIONf_chiral_restr0.075277
X-RAY DIFFRACTIONf_plane_restr0.008308
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3498-1.38360.39081230.35482806292988
1.3836-1.4210.28951250.24122922304791
1.421-1.46280.22251310.15232951308292
1.4628-1.510.17631280.1293010313894
1.51-1.5640.17391330.11333051318495
1.564-1.62660.16961350.11193086322196
1.6266-1.70060.17431350.11463096323196
1.7006-1.79020.16231390.11263101324096
1.7902-1.90230.15271440.11493151329597
1.9023-2.04910.1691430.12113225336899
2.0491-2.25510.13551460.11953240338699
2.2551-2.58110.14481440.120532753419100
2.5811-3.25030.18141470.132633233470100
3.2503-22.76850.14981560.14553447360399

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