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- PDB-3hwo: Crystal structure of Escherichia coli enterobactin-specific isoch... -

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Basic information

Entry
Database: PDB / ID: 3hwo
TitleCrystal structure of Escherichia coli enterobactin-specific isochorismate synthase EntC in complex with isochorismate
ComponentsIsochorismate synthase entC
KeywordsISOMERASE / isochorismate synthase / EntC / chorismate-utilizing enzymes / siderophore / enterobactin / Enterobactin biosynthesis / Ion transport / Iron / Iron transport / Transport
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 / SYNCHROTRON / SIR / Resolution: 2.3 Å
AuthorsSridharan, S. / Blundell, T.L.
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. / Blaszczyk, M. / Abell, C. / Blundell, T.L.
History
DepositionJun 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Non-polymer description
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr1_label_seq_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.ptnr3_label_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)87,0678
Polymers86,5172
Non-polymers5506
Water4,720262
1
A: Isochorismate synthase entC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5344
Polymers43,2591
Non-polymers2753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isochorismate synthase entC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5344
Polymers43,2591
Non-polymers2753
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: 43258.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b0593, entC, JW0585 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEJ2, isochorismate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 12% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2911
SYNCHROTRONSRS PX10.120.979
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
ReflectionResolution: 2.3→42.6 Å / Num. all: 41738 / Num. obs: 41380 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.3 Å / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIR / Resolution: 2.3→42.6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.475 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.304 / ESU R Free: 0.237
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25559 2088 5 %RANDOM
Rwork0.19991 ---
obs0.20271 39292 99.7 %-
all-41380 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.326 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5856 0 36 262 6154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226022
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9688190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4823.577274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14715971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2341552
X-RAY DIFFRACTIONr_chiral_restr0.0920.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024658
X-RAY DIFFRACTIONr_nbd_refined0.2370.32833
X-RAY DIFFRACTIONr_nbtor_refined0.3180.54074
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.5489
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4120.525
X-RAY DIFFRACTIONr_mcbond_it2.73953855
X-RAY DIFFRACTIONr_mcangle_it4.13176118
X-RAY DIFFRACTIONr_scbond_it5.48892380
X-RAY DIFFRACTIONr_scangle_it7.475112072
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 175 -
Rwork0.29 2772 -
obs--97.26 %

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