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- PDB-5jxz: A low magnesium structure of the isochorismate synthase, EntC -

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Basic information

Entry
Database: PDB / ID: 5jxz
TitleA low magnesium structure of the isochorismate synthase, EntC
ComponentsIsochorismate synthase EntC
KeywordsISOMERASE / chorismate / 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 / Chem-ISJ / Isochorismate synthase EntC
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 Center for Research Resources (NIH/NCRR)P20 RR016475 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 4, 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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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)86,9068
Polymers85,9532
Non-polymers9536
Water4,846269
1
A: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4534
Polymers42,9761
Non-polymers4773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4534
Polymers42,9761
Non-polymers4773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.205, 80.205, 272.200
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-ISJ / (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid / Chorismic 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.: 269 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298.15 K / Method: microbatch / pH: 6
Details: 0.1 M MES pH 6.0, 63% 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: 1.1 Å
DetectorType: ADSC QUANTUM 315 / 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: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.88→39.49 Å / Num. obs: 73403 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rsym value: 0.081 / Net I/σ(I): 14
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 2 / % possible all: 96.4

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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: 1.88→39.487 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.23
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1998 2.73 %Random selection
Rwork0.1871 ---
obs0.1882 73207 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.61 Å2
Refinement stepCycle: LAST / Resolution: 1.88→39.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 66 269 6049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135920
X-RAY DIFFRACTIONf_angle_d1.1188028
X-RAY DIFFRACTIONf_dihedral_angle_d14.5443586
X-RAY DIFFRACTIONf_chiral_restr0.063903
X-RAY DIFFRACTIONf_plane_restr0.0081065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8798-1.92680.31131360.2594840X-RAY DIFFRACTION97
1.9268-1.97890.26591400.23254972X-RAY DIFFRACTION100
1.9789-2.03710.22851410.20265026X-RAY DIFFRACTION100
2.0371-2.10290.25241410.19255021X-RAY DIFFRACTION100
2.1029-2.1780.22621400.18165018X-RAY DIFFRACTION100
2.178-2.26520.21351400.17075032X-RAY DIFFRACTION100
2.2652-2.36830.19371430.16765059X-RAY DIFFRACTION100
2.3683-2.49320.22061420.16585049X-RAY DIFFRACTION100
2.4932-2.64930.24241410.17015065X-RAY DIFFRACTION100
2.6493-2.85380.18511440.1665108X-RAY DIFFRACTION100
2.8538-3.14090.20231440.17145108X-RAY DIFFRACTION100
3.1409-3.59520.21611440.17585169X-RAY DIFFRACTION100
3.5952-4.52850.22031480.1755230X-RAY DIFFRACTION100
4.5285-39.49620.26361540.22245512X-RAY DIFFRACTION100

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