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- PDB-5jy8: An iron-bound structure of the isochorismate synthase EntC -

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Basic information

Entry
Database: PDB / ID: 5jy8
TitleAn iron-bound structure of the isochorismate synthase EntC
ComponentsIsochorismate synthase EntC
KeywordsISOMERASE
Function / homology
Function and homology information


isochorismate synthase / isochorismate synthase activity / enterobactin biosynthetic process / magnesium ion binding
Similarity search - Function
Isochorismate synthase / Anthranilate synthase / Anthranilate synthase / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-ISJ / Isochorismate synthase EntC
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.942 Å
AuthorsMeneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Lamb, A.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI77725 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K02 AI093675 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM116957 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: An Open and Shut Case: The Interaction of Magnesium with MST Enzymes.
Authors: Meneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Moran, G.R. / Lamb, A.L.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isochorismate synthase EntC
B: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6298
Polymers85,9532
Non-polymers6766
Water0
1
A: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3144
Polymers42,9761
Non-polymers3383
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3144
Polymers42,9761
Non-polymers3383
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.377, 81.377, 262.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Isochorismate synthase EntC / Isochorismate mutase


Mass: 42976.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: entC, Z0735, ECs0632 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AEJ3, isochorismate synthase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ISJ / (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid / Chorismic Acid / Chorismic acid


Mass: 226.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O6

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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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 298.15 K / Method: microbatch / pH: 6
Details: 0.1 M MES pH 6.0, 60% PEG 200, 0.05 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.739 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2015 / Details: Mirror: Rh coated flat mirror
RadiationMonochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.739 Å / Relative weight: 1
ReflectionResolution: 2.94→38.86 Å / Num. obs: 19603 / % possible obs: 99.4 % / Redundancy: 27.6 % / CC1/2: 0.998 / Rsym value: 0.167 / Net I/σ(I): 21.6
Reflection shellResolution: 2.94→3.12 Å / Redundancy: 27.3 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 5.6 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HWO

3hwo


Resolution: 2.942→38.861 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1952 10 %Random selection
Rwork0.2116 ---
obs0.2163 19521 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.942→38.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5663 0 36 0 5699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045822
X-RAY DIFFRACTIONf_angle_d0.7667918
X-RAY DIFFRACTIONf_dihedral_angle_d13.5583532
X-RAY DIFFRACTIONf_chiral_restr0.045889
X-RAY DIFFRACTIONf_plane_restr0.0061054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.942-3.01560.36551270.26521152X-RAY DIFFRACTION93
3.0156-3.09710.33651360.22271217X-RAY DIFFRACTION100
3.0971-3.18820.29381380.22361232X-RAY DIFFRACTION100
3.1882-3.2910.251360.2121235X-RAY DIFFRACTION100
3.291-3.40860.25421370.22281235X-RAY DIFFRACTION100
3.4086-3.5450.27631390.22151242X-RAY DIFFRACTION100
3.545-3.70620.261380.20511245X-RAY DIFFRACTION100
3.7062-3.90140.27371380.20281241X-RAY DIFFRACTION100
3.9014-4.14560.22751390.20081245X-RAY DIFFRACTION100
4.1456-4.46520.21021380.17921254X-RAY DIFFRACTION100
4.4652-4.91380.20051410.17481276X-RAY DIFFRACTION100
4.9138-5.6230.26581420.20861276X-RAY DIFFRACTION100
5.623-7.07740.26661450.24031307X-RAY DIFFRACTION100
7.0774-38.86440.26681580.2351412X-RAY DIFFRACTION100

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