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- PDB-5jy4: A high magnesium structure of the isochorismate synthase, EntC -

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Basic information

Entry
Database: PDB / ID: 5jy4
TitleA high magnesium structure of the isochorismate synthase, EntC
Components(Isochorismate synthase EntC) x 2
KeywordsISOMERASE / isochorismate
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-ISC / Isochorismate synthase EntC
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)86,4706
Polymers85,9692
Non-polymers5014
Water2,522140
1
A: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2433
Polymers42,9921
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2273
Polymers42,9761
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.907, 80.907, 265.231
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: 42992.469 Da / Num. of mol.: 1
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: Protein Isochorismate synthase EntC / Isochorismate mutase


Mass: 42976.469 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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.: 2 / Source method: obtained synthetically / Formula: C10H10O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 298.15 K / Method: microbatch / pH: 6.2
Details: 0.1 M MES pH 6.2, 50% PEG 200, 0.05 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2016 / Details: Mirror: Rh coated
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.11→38.9 Å / Num. obs: 51991 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rsym value: 0.074 / Net I/σ(I): 14.5
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.031 / Mean I/σ(I) obs: 2 / % possible all: 97.8

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Processing

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

3hwo


Resolution: 2.11→38.898 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 2000 3.85 %Random selection
Rwork0.2007 ---
obs0.2026 51881 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.71 Å2
Refinement stepCycle: LAST / Resolution: 2.11→38.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 34 140 5964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145953
X-RAY DIFFRACTIONf_angle_d1.2738094
X-RAY DIFFRACTIONf_dihedral_angle_d12.3493619
X-RAY DIFFRACTIONf_chiral_restr0.065905
X-RAY DIFFRACTIONf_plane_restr0.0091077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1073-2.160.31081380.2593424X-RAY DIFFRACTION98
2.16-2.21840.33991410.25753511X-RAY DIFFRACTION100
2.2184-2.28370.31291390.24793494X-RAY DIFFRACTION100
2.2837-2.35740.29511410.23393505X-RAY DIFFRACTION100
2.3574-2.44160.27171410.22633526X-RAY DIFFRACTION100
2.4416-2.53940.28771410.22243526X-RAY DIFFRACTION100
2.5394-2.65490.30531420.21973520X-RAY DIFFRACTION100
2.6549-2.79480.33971420.2083556X-RAY DIFFRACTION100
2.7948-2.96990.23351420.20993536X-RAY DIFFRACTION100
2.9699-3.19910.24611430.20173554X-RAY DIFFRACTION100
3.1991-3.52090.2341440.20073602X-RAY DIFFRACTION100
3.5209-4.02990.23251440.18373614X-RAY DIFFRACTION100
4.0299-5.07540.20341470.16963645X-RAY DIFFRACTION99
5.0754-38.90460.24561550.20233868X-RAY DIFFRACTION99

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