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- PDB-5xo0: Crystal structure of the isochorismatase domain of AngB from Vibr... -

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Basic information

Entry
Database: PDB / ID: 5xo0
TitleCrystal structure of the isochorismatase domain of AngB from Vibrio anguillarum 775
ComponentsIschorismate lyase
KeywordsHYDROLASE / isochorismatase / DHBA / siderophore synthesis / iron metabolism
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: 1.85 Å
AuthorsMa, Q. / Du, J.
Funding support China, 4items
OrganizationGrant numberCountry
1000 talents program China
100 talents program, CAS China
aoshan talents2015ASTP 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

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Assembly

Deposited unit
A: Ischorismate lyase
B: Ischorismate lyase


Theoretical massNumber of molelcules
Total (without water)48,8742
Polymers48,8742
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-25 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.250, 140.250, 59.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ischorismate lyase


Mass: 24436.768 Da / Num. of mol.: 2 / Fragment: UNP residues 1-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio anguillarum 775 (bacteria) / Strain: 775 / Gene: G, angB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6W4P9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 2% PEG 400, 2M Li2SO4 at 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2015 / Details: dynamically bendable toroidal mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.847→121.457 Å / Num. obs: 52566 / % possible obs: 91.3 % / Redundancy: 21.6 % / Biso Wilson estimate: 27.89 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.024 / Rsym value: 0.108 / Net I/σ(I): 25.3
Reflection shellResolution: 1.847→1.853 Å / Redundancy: 21.3 % / Rmerge(I) obs: 1.784 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 578 / CC1/2: 0.736 / Rpim(I) all: 0.394 / Rsym value: 1.784 / % possible all: 96

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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: 3TB4

3tb4


Resolution: 1.85→27.09 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.907 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.123 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.114 / Details: TLS parameters are refined for each chain.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2635 5.05 %RANDOM
Rwork0.2 ---
obs0.201 52156 91.1 %-
Displacement parametersBiso mean: 31.65 Å2
Baniso -1Baniso -2Baniso -3
1-6.8447 Å20 Å20 Å2
2--6.8447 Å20 Å2
3----13.6894 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 1.85→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 0 343 3659
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013398HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034634HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1148SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes476HARMONIC5
X-RAY DIFFRACTIONt_it3398HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion15.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion452SEMIHARMONIC5
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_contact4272SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 114 4.93 %
Rwork0.257 2197 -
all0.257 2311 -
obs--55.12 %
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)
10.9097-0.2146-0.08851.3734-0.20620.8030.0220.03830.0548-0.07330.00380.1719-0.0794-0.0672-0.0259-0.10230.0101-0.0244-0.1599-0.0044-0.151961.03214.95149.5627
21.00570.0741-0.03711.70990.05330.567-0.04080.09050.0555-0.1726-0.034-0.3908-0.0760.14690.0748-0.1135-0.02870.0236-0.1640.0097-0.043388.795513.65337.974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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