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- PDB-5jzd: A re-refinement of the isochorismate synthase EntC -

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Basic information

Entry
Database: PDB / ID: 5jzd
TitleA re-refinement of the isochorismate synthase EntC
ComponentsIsochorismate synthase EntC
KeywordsISOMERASE / isochorismate synthase / 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 / Isochorismate synthase EntC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.303 Å
AuthorsMeneely, K.M. / Lamb, A.L.
Funding support United States, 2items
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
CitationJournal: J. Mol. Biol. / Year: 2010
Title: Crystal structure of Escherichia coli enterobactin-specific isochorismate synthase (EntC) bound to its reaction product isochorismate: implications for the enzyme mechanism and differential ...Title: Crystal structure of Escherichia coli enterobactin-specific isochorismate synthase (EntC) bound to its reaction product isochorismate: implications for the enzyme mechanism and differential activity of chorismate-utilizing enzymes.
Authors: Sridharan, S. / Howard, N. / Kerbarh, O. / Baszczyk, M. / Abell, C. / Blundell, T.L.
History
DepositionMay 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Mar 15, 2017Group: Other
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 0THIS ENTRY 5JZD REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 3HWO. ORIGINAL DATA ...THIS ENTRY 5JZD REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 3HWO. ORIGINAL DATA DETERMINED BY AUTHORS S.SRIDHARAN, T.L. BLUNDELL

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,4546
Polymers85,9532
Non-polymers5014
Water1,40578
1
A: 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
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)62.469, 104.795, 140.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
Details: re-refined entry, data collected by original depositors None entered here
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: entC, b0593, JW0585 / References: UniProt: P0AEJ2, isochorismate synthase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.67 Å3/Da / Density % sol: 53.86 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3HWO

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PHENIX / Version: (1.10_2155) / Classification: refinement
RefinementResolution: 2.303→41.949 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 26.97
Details: Refinement was done with simulated annealing in Phenix Refine
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 2088 5.05 %Random selection
Rwork0.1953 ---
obs0.1984 41374 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.303→41.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5843 0 34 78 5955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136009
X-RAY DIFFRACTIONf_angle_d1.2878173
X-RAY DIFFRACTIONf_dihedral_angle_d16.5283653
X-RAY DIFFRACTIONf_chiral_restr0.062913
X-RAY DIFFRACTIONf_plane_restr0.011089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3026-2.35610.33211550.28842462X-RAY DIFFRACTION97
2.3561-2.4150.29321400.2622611X-RAY DIFFRACTION100
2.415-2.48030.33691410.26222565X-RAY DIFFRACTION100
2.4803-2.55330.34061440.25582603X-RAY DIFFRACTION100
2.5533-2.63570.28881320.242585X-RAY DIFFRACTION100
2.6357-2.72990.27831320.2362621X-RAY DIFFRACTION100
2.7299-2.83920.32591480.23542601X-RAY DIFFRACTION100
2.8392-2.96830.31151320.23152601X-RAY DIFFRACTION100
2.9683-3.12480.31141230.23162646X-RAY DIFFRACTION100
3.1248-3.32050.27371440.2072580X-RAY DIFFRACTION100
3.3205-3.57670.22821240.20162639X-RAY DIFFRACTION100
3.5767-3.93640.25061300.17782663X-RAY DIFFRACTION100
3.9364-4.50550.20071560.15472640X-RAY DIFFRACTION100
4.5055-5.67420.20931470.15792676X-RAY DIFFRACTION100
5.6742-41.95590.24141400.16482793X-RAY DIFFRACTION99

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