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Entry
Database: PDB / ID: 1com
TitleTHE MONOFUNCTIONAL CHORISMATE MUTASE FROM BACILLUS SUBTILIS: STRUCTURE DETERMINATION OF CHORISMATE MUTASE AND ITS COMPLEXES WITH A TRANSITION STATE ANALOG AND PREPHENATE, AND IMPLICATIONS ON THE MECHANISM OF ENZYMATIC REACTION
ComponentsCHORISMATE MUTASE
KeywordsCHORISMATE MUTASE
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
Similarity search - Function
Chorismate mutase, AroH class / Chorismate mutase type I / Chorismate mutase domain profile. / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PREPHENIC ACID / Chorismate mutase AroH
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsChook, Y.M. / Ke, H. / Lipscomb, W.N.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: The monofunctional chorismate mutase from Bacillus subtilis. Structure determination of chorismate mutase and its complexes with a transition state analog and prephenate, and implications for ...Title: The monofunctional chorismate mutase from Bacillus subtilis. Structure determination of chorismate mutase and its complexes with a transition state analog and prephenate, and implications for the mechanism of the enzymatic reaction.
Authors: Chook, Y.M. / Gray, J.V. / Ke, H. / Lipscomb, W.N.
History
DepositionApr 8, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CHORISMATE MUTASE
B: CHORISMATE MUTASE
C: CHORISMATE MUTASE
D: CHORISMATE MUTASE
E: CHORISMATE MUTASE
F: CHORISMATE MUTASE
G: CHORISMATE MUTASE
H: CHORISMATE MUTASE
I: CHORISMATE MUTASE
J: CHORISMATE MUTASE
K: CHORISMATE MUTASE
L: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,13121
Polymers174,09512
Non-polymers2,0369
Water9,062503
1
A: CHORISMATE MUTASE
B: CHORISMATE MUTASE
C: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2026
Polymers43,5243
Non-polymers6793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-22 kcal/mol
Surface area13840 Å2
MethodPISA
2
J: CHORISMATE MUTASE
K: CHORISMATE MUTASE
L: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7504
Polymers43,5243
Non-polymers2261
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-36 kcal/mol
Surface area14060 Å2
MethodPISA
3
D: CHORISMATE MUTASE
E: CHORISMATE MUTASE
F: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2026
Polymers43,5243
Non-polymers6793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-23 kcal/mol
Surface area13970 Å2
MethodPISA
4
G: CHORISMATE MUTASE
H: CHORISMATE MUTASE
I: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9765
Polymers43,5243
Non-polymers4522
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-30 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.400, 68.300, 102.800
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.40172, 0.7539, 0.51985), (-0.15728, 0.50244, -0.85018), (-0.90216, -0.4233, -0.08326)
Vector: 17.3616, 52.3834, 89.9799)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. SIMILAR TRANSFORMATIONS WILL TRANSFORM CHAIN *C* ONTO *B* AND CHAIN *A* ONTO *C*.

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Components

#1: Protein
CHORISMATE MUTASE /


Mass: 14507.915 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / References: UniProt: P19080, chorismate mutase
#2: Chemical
ChemComp-PRE / PREPHENIC ACID / Prephenic acid


Mass: 226.183 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H10O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.3 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein11
25 mMTris-HCl12
31 mMbeta-mercaptoethanol12
40.5 mM12NaN3
50.1 mMEDTA12
611-12 %(w/v)PEG335012

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 80528 / % possible obs: 75 % / Num. measured all: 208894 / Rmerge(I) obs: 0.055

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.179 / Rfactor obs: 0.179 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13511 0 153 1509 15173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.84

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