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- PDB-2fp2: Secreted Chorismate Mutase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2fp2
TitleSecreted Chorismate Mutase from Mycobacterium tuberculosis
ComponentsChorismate mutase
KeywordsISOMERASE / alpha-helical
Function / homology
Function and homology information


salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / extracellular region
Similarity search - Function
Chorismate mutase, periplasmic / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Chorismate mutase, periplasmic / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-TSA / Secreted chorismate mutase / Secreted chorismate mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsOkvist, M. / Dey, R. / Sasso, S. / Grahn, E. / Kast, P. / Krengel, U.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: 1.6A Crystal Structure of the Secreted Chorismate Mutase from Mycobacterium tuberculosis: Novel Fold Topology Revealed
Authors: Okvist, M. / Dey, R. / Sasso, S. / Grahn, E. / Kast, P. / Krengel, U.
History
DepositionJan 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 30, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2193
Polymers36,9912
Non-polymers2281
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.906, 72.800, 61.716
Angle α, β, γ (deg.)90.00, 103.99, 90.00
Int Tables number4
Space group name H-MP1211
DetailsProposed to be the dimer in the asymmetric unit

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Components

#1: Protein Chorismate mutase


Mass: 18495.512 Da / Num. of mol.: 2 / Fragment: residues 34-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pKTU3-HT / Production host: Escherichia coli (E. coli) / Strain (production host): KA29
References: UniProt: O07746, UniProt: P9WIB9*PLUS, chorismate mutase
#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.: 1 / Source method: obtained synthetically / Formula: C10H12O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5-15% PEG 4000, 0.2 M sodium acetate, 0.1 M cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.087 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 1.64→38.92 Å / Num. all: 45129 / Num. obs: 45129 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.4
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 7.3 / Num. unique all: 6328 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FP1

2fp1


Resolution: 1.64→38.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.519 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20333 2284 5.1 %RANDOM
Rwork0.17016 ---
all0.17179 42905 --
obs0.17179 42905 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.726 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.18 Å2
2--0.49 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.091 Å0.09 Å
Luzzati sigma a-0.054 Å
Refinement stepCycle: LAST / Resolution: 1.64→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 16 416 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212750
X-RAY DIFFRACTIONr_bond_other_d0.0070.021904
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9643773
X-RAY DIFFRACTIONr_angle_other_deg0.9123.0024626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8035354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82123.381139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82715455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7521532
X-RAY DIFFRACTIONr_chiral_restr0.0810.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
X-RAY DIFFRACTIONr_nbd_refined0.2350.2657
X-RAY DIFFRACTIONr_nbd_other0.210.22080
X-RAY DIFFRACTIONr_nbtor_refined0.180.21396
X-RAY DIFFRACTIONr_nbtor_other0.0870.21352
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8271.52230
X-RAY DIFFRACTIONr_mcbond_other0.2691.5650
X-RAY DIFFRACTIONr_mcangle_it1.5722761
X-RAY DIFFRACTIONr_scbond_it2.79431195
X-RAY DIFFRACTIONr_scangle_it4.2494.51000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.637→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 164 -
Rwork0.239 2978 -
obs--93.48 %

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