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- PDB-1dbf: CHORISMATE MUTASE FROM BACILLUS SUBTILIS AT 1.30 ANGSTROM -

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Basic information

Entry
Database: PDB / ID: 1dbf
TitleCHORISMATE MUTASE FROM BACILLUS SUBTILIS AT 1.30 ANGSTROM
ComponentsPROTEIN (CHORISMATE MUTASE)
KeywordsISOMERASE / CHORISMATE MUTASE / SHIKIMATE PATHWAY
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
Chorismate mutase AroH
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGilliland, G.L. / Ladner, J.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The 1.30 A resolution structure of the Bacillus subtilis chorismate mutase catalytic homotrimer.
Authors: Ladner, J.E. / Reddy, P. / Davis, A. / Tordova, M. / Howard, A.J. / Gilliland, G.L.
History
DepositionNov 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 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 / 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: PROTEIN (CHORISMATE MUTASE)
B: PROTEIN (CHORISMATE MUTASE)
C: PROTEIN (CHORISMATE MUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,84917
Polymers43,5243
Non-polymers1,32514
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-153 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.200, 83.770, 85.960
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 PROTEIN (CHORISMATE MUTASE)


Mass: 14507.915 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PRE1-AROQ / Production host: Escherichia coli (E. coli) / Strain (production host): MZ1 / References: UniProt: P19080, chorismate mutase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 1.87 Å3/Da / Density % sol: 43.01 %
Description: THE MODEL USED FOR MOLECULAR REPLACEMENT WAS ONE TRIMER (ABC) FROM STRUCTURE 2CHS. THE WATERS ARE GROUPED. WATERS 301-433 MAKE THEIR CLOSEST CONTACT WITH RESIDUES IN CHAIN A, WATERS 434- ...Description: THE MODEL USED FOR MOLECULAR REPLACEMENT WAS ONE TRIMER (ABC) FROM STRUCTURE 2CHS. THE WATERS ARE GROUPED. WATERS 301-433 MAKE THEIR CLOSEST CONTACT WITH RESIDUES IN CHAIN A, WATERS 434-567 WITH RESIDUES IN CHAIN B, WATERS 568-709 WITH RESIDUES IN CHAIN C, WATERS 710-717 WITH SO4 IONS AND WATERS 718- 724 WITH GLYCEROL MOLECULES. THE CLOSEST PROTEIN CHAIN FOR WATER MOLECULES 710, 711, 713, 715, 717, 718, 720, 722, 723, 724 IS CHAIN A. THE CLOSEST PROTEIN CHAIN FOR WATER MOLECULES 714 AND 719 IS CHAIN B. THE CLOSEST PROTEIN CHAIN FOR WATER MOLECULES 712, 716 AND 721 IS CHAIN C.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3
Details: PROTEIN DROP: 5 MICROLITERS PROTEIN SOLUTION, 5 MICROLITERS RESERVOIR. PROTEIN SOLUTION: 13 MG/ML PROTEIN, 100 MM PMSF, 100 MM NACL, 50 MM TRIS PH 7.5, 1 MM EDTA, 1 MM DTT. RESERVOIR ...Details: PROTEIN DROP: 5 MICROLITERS PROTEIN SOLUTION, 5 MICROLITERS RESERVOIR. PROTEIN SOLUTION: 13 MG/ML PROTEIN, 100 MM PMSF, 100 MM NACL, 50 MM TRIS PH 7.5, 1 MM EDTA, 1 MM DTT. RESERVOIR SOLUTION: 2.2 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE PH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
2100 mMsodium chloride1drop
350 mMTris-HCl1drop
41 mMdithiothreitol1drop
51 mMEDTA1drop
60.1 mMPMSF1drop
72.2 Mammonium sulfate1reservoir
8100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: BRUKER / Detector: CCD / Date: Feb 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 89868 / % possible obs: 78 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.5
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.2 / % possible all: 23
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 100 Å / % possible obs: 92 % / Redundancy: 2.8 % / Num. measured all: 255732
Reflection shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 11.34 Å / % possible obs: 68 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.336

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CHS

2chs


Resolution: 1.3→100 Å / Num. parameters: 3296 / Num. restraintsaints: 4047 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE EFFECTIVE RESOLUTION IS 1.30 ANGSTROMS, HOWEVER, ALL DATA AVAILABLE WERE USED DURING THE REFINEMENT. THIS INCLUDES SOME DATA AS HIGH AS 1.20 ANGSTROMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 9021 10 %RANDOM
all0.169 89868 --
obs0.167 -59.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973) 201-228
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3529
Refinement stepCycle: LAST / Resolution: 1.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 75 424 3529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0.027
X-RAY DIFFRACTIONs_from_restr_planes0.0284
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0.083

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