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- PDB-1ecm: ATOMIC STRUCTURE OF THE BURIED CATALYTIC POCKET OF ESCHERICHIA CO... -

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Basic information

Entry
Database: PDB / ID: 1ecm
TitleATOMIC STRUCTURE OF THE BURIED CATALYTIC POCKET OF ESCHERICHIA COLI CHORISMATE MUTASE
ComponentsENDO-OXABICYCLIC TRANSITION STATE ANALOGUE
KeywordsCHORISMATE MUTASE / P-PROTEIN / CHORISMATE MUTASE DOMAIN
Function / homology
Function and homology information


prephenate dehydratase / prephenate dehydratase activity / tyrosine biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / L-phenylalanine biosynthetic process / protein homodimerization activity / cytoplasm
Similarity search - Function
Chorismate mutase, gammaproteobacteria / Prephenate dehydratase signature 1. / Prephenate dehydratase signature 2. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / Chorismate mutase / Chorismate mutase domain superfamily ...Chorismate mutase, gammaproteobacteria / Prephenate dehydratase signature 1. / Prephenate dehydratase signature 2. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / ACT domain profile. / ACT domain / ACT-like domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-TSA / Bifunctional chorismate mutase/prephenate dehydratase / Bifunctional chorismate mutase/prephenate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsClardy, J. / Lee, A.Y.
CitationJournal: J.Am.Chem.Soc. / Year: 1995
Title: ATOMIC-STRUCTURE OF THE BURIED CATALYTIC POCKET OF ESCHERICHIA-COLI CHORISMATE MUTASE.
Authors: Lee, A.Y. / Karplus, P.A. / Ganem, B. / Clardy, J.
History
DepositionNov 28, 1994Processing site: BNL
Revision 1.0Dec 1, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: ENDO-OXABICYCLIC TRANSITION STATE ANALOGUE
B: ENDO-OXABICYCLIC TRANSITION STATE ANALOGUE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5564
Polymers25,0992
Non-polymers4562
Water1,38777
1
A: ENDO-OXABICYCLIC TRANSITION STATE ANALOGUE
B: ENDO-OXABICYCLIC TRANSITION STATE ANALOGUE
hetero molecules

A: ENDO-OXABICYCLIC TRANSITION STATE ANALOGUE
B: ENDO-OXABICYCLIC TRANSITION STATE ANALOGUE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1118
Polymers50,1994
Non-polymers9134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-26 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.830, 80.830, 83.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ENDO-OXABICYCLIC TRANSITION STATE ANALOGUE


Mass: 12549.651 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PJS47 / Cell line: NK6024 / References: UniProt: P07022, UniProt: P0A9J8*PLUS
#2: Chemical ChemComp-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID


Mass: 228.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSEE REFERENCE JACKSON, J.Y.; JACOBS, J.W.; SUGASAWARA, R.; REICH, S.H.; BARTLETT, P.A.; SCHULTZ, P. ...SEE REFERENCE JACKSON, J.Y.; JACOBS, J.W.; SUGASAWARA, R.; REICH, S.H.; BARTLETT, P.A.; SCHULTZ, P. G. J.AM.CHEM.SOC., 1988, 110, 4841. THE INHIBITOR IS THE SAME AS THAT IN THE PDB ENTRY 2CHS AND 1FIG.
Source detailsTHE PROTEIN: THE N-TERMINAL 109 AMINO ACIDS OF P-PROTEIN (P FOR PHENYLALANINE) SEE REFERENCE: ...THE PROTEIN: THE N-TERMINAL 109 AMINO ACIDS OF P-PROTEIN (P FOR PHENYLALANINE) SEE REFERENCE: STEWART, J.; WILSON, D. B.; GANEM, B. J. AM. CHEM. SOC., 1990 112, 4582.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal grow
*PLUS
pH: 6.85 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.5 mg/mlprotein-inhibitor solution1drop
2100 mMsodium cacodylate1reservoir
3200 mMsodium acetate1reservoir
428-30 %PEG80001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 23622 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.231 --
Rwork0.192 --
obs0.192 15182 94.8 %
Displacement parametersBiso mean: 44.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 32 77 1622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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