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- PDB-2w19: Non-covalent complex between dahp synthase and chorismate mutase ... -

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Basic information

Entry
Database: PDB / ID: 2w19
TitleNon-covalent complex between dahp synthase and chorismate mutase from Mycobacterium tuberculosis
Components
  • 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
  • CHORISMATE MUTASE
KeywordsTRANSFERASE/ISOMERASE / TRANSFERASE-ISOMERASE COMPLEX / TRANSFERASE ISOMERASE COMPLEX / AROMATIC AMINO ACID BIOSYNTHESIS / MULTI-ENZYME COMPLEX / PROTEIN-PROTEIN INTERACTIONS / ENZYME ACTIVATION / FEEDBACK REGULATION / SHIKIMATE PATHWAY / COMPLEX FORMATION / MYCOBACTERIUM TUBERCULOSIS RV0948C / ISOMERASE / TRANSFERASE / DRUG TARGET / ENZYME CATALYSIS
Function / homology
Function and homology information


aromatic amino acid family biosynthetic process, prephenate pathway / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process ...aromatic amino acid family biosynthetic process, prephenate pathway / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chorismate mutase, high GC Gram-positive bacteria/archaeal / : / DAHP synthetase, class II / Class-II DAHP synthetase family / 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, high GC Gram-positive bacteria/archaeal / : / DAHP synthetase, class II / Class-II DAHP synthetase family / 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 / Aldolase-type TIM barrel / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phospho-2-dehydro-3-deoxyheptonate aldolase AroG / Intracellular chorismate mutase / Intracellular chorismate mutase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOkvist, M. / Sasso, S. / Roderer, K. / Gamper, M. / Codoni, G. / Krengel, U. / Kast, P.
CitationJournal: Embo J. / Year: 2009
Title: Structure and Function of a Complex between Chorismate Mutase and Dahp Synthase: Efficiency Boost for the Junior Partner.
Authors: Sasso, S. / Okvist, M. / Roderer, K. / Gamper, M. / Codoni, G. / Krengel, U. / Kast, P.
History
DepositionOct 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
B: 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
C: CHORISMATE MUTASE
D: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,30018
Polymers123,9994
Non-polymers1,30114
Water6,323351
1
A: 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
B: 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
C: CHORISMATE MUTASE
D: CHORISMATE MUTASE
hetero molecules

A: 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
B: 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
C: CHORISMATE MUTASE
D: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,60036
Polymers247,9978
Non-polymers2,60228
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area27320 Å2
ΔGint-180.9 kcal/mol
Surface area86550 Å2
MethodPQS
Unit cell
Length a, b, c (Å)204.018, 204.018, 66.513
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2057-

HOH

21B-2064-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 462
2114B3 - 462
1124C18 - 90
2124D18 - 90

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.471323, -0.835732, -0.281794), (-0.84155, -0.521761, 0.139856), (-0.263911, 0.171226, -0.949227)101.971, 179, -1.132
2given(0.459088, -0.84594, -0.271338), (-0.846812, -0.509036, 0.154247), (-0.268605, 0.158959, -0.950044)103.095, 178.164, -0.21

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Components

#1: Protein 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG / DAHP SYNTHETASE / PHENYLALANINE-REPRESSIBLE


Mass: 51891.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PKTDS-HN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KA13
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase
#2: Protein CHORISMATE MUTASE / RV0948C/MT0975


Mass: 10107.812 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PKTCMM-H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KA13
References: UniProt: P64767, UniProt: P9WIC1*PLUS, chorismate mutase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINALLY HIS-TAGGED MTDS (472 RESIDUES)

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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: 3 Å3/Da / Density % sol: 52.4 % / Description: NONE
Crystal growpH: 7.9
Details: 0.9M AMMONIUM SULFATE, 0.1M TRIS PH 7.9, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.15→66.82 Å / Num. obs: 83270 / % possible obs: 96.6 % / Observed criterion σ(I): -3.7 / Redundancy: 6.84 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.26
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.93 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B7O

2b7o


Resolution: 2.15→66.82 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.204 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21115 4163 5 %RANDOM
Rwork0.17805 ---
obs0.17971 79086 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.15→66.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7519 0 81 351 7951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217721
X-RAY DIFFRACTIONr_bond_other_d0.0020.025280
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.97710459
X-RAY DIFFRACTIONr_angle_other_deg0.938312805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90322.824340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.332151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3121581
X-RAY DIFFRACTIONr_chiral_restr0.0670.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021530
X-RAY DIFFRACTIONr_nbd_refined0.1930.21557
X-RAY DIFFRACTIONr_nbd_other0.1960.25646
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23703
X-RAY DIFFRACTIONr_nbtor_other0.0840.23976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2340
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A5325medium positional0.570.5
12B5325medium positional0.570.5
21C947medium positional0.30.5
22D947medium positional0.30.5
11A5325medium thermal0.572
12B5325medium thermal0.572
21C947medium thermal0.192
22D947medium thermal0.192
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 232 -
Rwork0.253 4675 -
obs--77.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7605-0.1544-0.35540.75080.20280.810.0327-0.06350.17770.00690.0255-0.1679-0.11340.1151-0.0582-0.05570.0108-0.013-0.1058-0.0293-0.125839.1554114.066615.7732
20.9783-0.58780.25131.280.04190.69580.029-0.0361-0.1670.035-0.01380.07910.065-0.0586-0.0152-0.15260.0042-0.0027-0.091-0.0059-0.157220.648289.3722-7.5448
35.0239-0.7042-1.91173.27670.3292.79250.1221-0.3560.28450.10320.019-0.0749-0.33110.0851-0.14110.3017-0.06370.03730.2225-0.07720.428368.157132.15935.9543
42.542-1.89810.65594.1047-0.72192.73960.16670.0315-0.4197-0.33280.00660.35090.2381-0.1709-0.17330.1565-0.0887-0.06230.15920.00370.388622.015852.6447-3.1097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 462
2X-RAY DIFFRACTION2B23 - 462
3X-RAY DIFFRACTION3C12 - 90
4X-RAY DIFFRACTION4D12 - 90

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