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- PDB-5xo1: Crystal structure of the isochorismatase domain of VabB from Vibr... -

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Basic information

Entry
Database: PDB / ID: 5xo1
TitleCrystal structure of the isochorismatase domain of VabB from Vibrio anguillarum 775
ComponentsIsochorismate lyase
KeywordsHYDROLASE / VabB / isochorismatase / siderophore / iron
Function / homology
Function and homology information


isochorismatase / isochorismatase activity / lyase 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
Biological speciesVibrio anguillarum 775 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMa, Q. / Du, J.
Funding support China, 4items
OrganizationGrant numberCountry
1000 talents program China
100 talents program, CAS China
aoshan talentsNo. 2015ASTP China
postdoctorial science foundation2015M572091 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2017
Title: Crystal structures of the isochorismatase domains from Vibrio anguillarum.
Authors: Du, J. / Deng, T. / Ma, Q.
History
DepositionMay 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isochorismate lyase
B: Isochorismate lyase
C: Isochorismate lyase
D: Isochorismate lyase
E: Isochorismate lyase
F: Isochorismate lyase


Theoretical massNumber of molelcules
Total (without water)148,6946
Polymers148,6946
Non-polymers00
Water3,153175
1
A: Isochorismate lyase
B: Isochorismate lyase


Theoretical massNumber of molelcules
Total (without water)49,5652
Polymers49,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-21 kcal/mol
Surface area16710 Å2
MethodPISA
2
C: Isochorismate lyase
D: Isochorismate lyase


Theoretical massNumber of molelcules
Total (without water)49,5652
Polymers49,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-20 kcal/mol
Surface area16570 Å2
MethodPISA
3
E: Isochorismate lyase
F: Isochorismate lyase


Theoretical massNumber of molelcules
Total (without water)49,5652
Polymers49,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-21 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.854, 174.005, 49.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Isochorismate lyase


Mass: 24782.371 Da / Num. of mol.: 6 / Fragment: UNP residues 1-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio anguillarum 775 (bacteria) / Strain: 775 / Gene: vabB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5DK16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 8000, 0.1M imidazole, 0.2M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2016 / Details: dynamically bendable toroidal mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.23→143.85 Å / Num. obs: 61526 / % possible obs: 99.6 % / Redundancy: 14 % / Biso Wilson estimate: 49.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Rsym value: 0.12 / Net I/σ(I): 14.5
Reflection shellResolution: 2.23→2.238 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.189 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 588 / CC1/2: 0.627 / Rpim(I) all: 0.357 / Rsym value: 1.189 / % possible all: 90.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
autoPROC1.0.4data reduction
autoPROC1.0.4data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XO0

5xo0


Resolution: 2.23→32.65 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.19
Details: TLS parameters are refined for each chain. Thin shell test set is used.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3058 4.98 %Thin shells
Rwork0.193 ---
obs0.194 61425 99.5 %-
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.1086 Å20 Å20 Å2
2---5.7917 Å20 Å2
3---3.6831 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.23→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9757 0 0 175 9932
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110004HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0913623HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3402SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes250HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1415HARMONIC5
X-RAY DIFFRACTIONt_it10004HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion19.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1346SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11449SEMIHARMONIC4
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.224 4246 -
all0.224 4246 -
obs--94.14 %
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)
12.997-0.60590.65732.4176-0.32351.05310.1007-0.0634-0.20140.037-0.02020.19220.0728-0.0157-0.0805-0.18390.0887-0.0141-0.12460.0108-0.059352.73686.589670.2958
23.5556-0.81660.38582.6997-0.856520.11460.4580.7695-0.03-0.3707-0.5671-0.16680.29950.2561-0.24540.07020.0498-0.19670.1490.080368.51526.834560.2346
32.1256-0.3489-0.26212.0899-0.30781.6235-0.0098-0.1912-0.15340.08990.09010.206-0.1951-0.2184-0.0802-0.15410.0824-0.0114-0.03990.0267-0.152513.395133.686964.6892
43.083-1.50650.80682.2246-0.27032.15340.45150.527-0.9009-0.4548-0.19530.51230.33780.1113-0.2563-0.13210.1456-0.1931-0.1247-0.1460.011823.808312.341750.4599
52.5824-0.30480.70791.5716-0.56161.4972-0.06010.20030.3338-0.21510.0048-0.0385-0.14430.1140.0553-0.103-0.0054-0.0095-0.07840.0183-0.145930.713259.94648.2174
63.36090.0393-0.30531.80670.12072.8283-0.0305-0.2140.4864-0.0490.0207-0.5492-0.10610.70320.0097-0.3336-0.0213-0.01330.0422-0.0413-0.025454.343159.305862.665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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