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- PDB-2w1a: Non-covalent complex between dahp synthase and chorismate mutase ... -

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Basic information

Entry
Database: PDB / ID: 2w1a
TitleNon-covalent complex between dahp synthase and chorismate mutase from Mycobacterium tuberculosis with bound tsa
Components
  • 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
  • CHORISMATE MUTASE
KeywordsTRANSFERASE/ISOMERASE / TRANSFERASE-ISOMERASE COMPLEX / AROMATIC AMINO ACID BIOSYNTHESIS / MULTI-ENZYME COMPLEX / PROTEIN-PROTEIN INTERACTIONS / SHIKIMATE PATHWAY
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 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, high GC Gram-positive bacteria/archaeal / DAHP synthetase, class II / Class-II DAHP synthetase family / 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 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
O-DODECANYL OCTAETHYLENE GLYCOL / : / Chem-TSA / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG / Intracellular chorismate mutase / Intracellular chorismate mutase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.35 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 1.1Apr 11, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)125,86216
Polymers123,9994
Non-polymers1,86412
Water3,855214
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)251,72532
Polymers247,9978
Non-polymers3,72724
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area30260 Å2
ΔGint-188.3 kcal/mol
Surface area90070 Å2
MethodPQS
Unit cell
Length a, b, c (Å)205.910, 205.910, 67.240
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-2036-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.467531, -0.838453, -0.28002), (-0.843062, -0.518186, 0.143978), (-0.265821, 0.16876, -0.949136)103.35, 180.584, -0.915
2given(0.464172, -0.845132, -0.265133), (-0.844764, -0.512395, 0.154358), (-0.266306, 0.152326, -0.951776)104.038, 180.17, 0.084

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Components

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Protein , 2 types, 4 molecules ABCD

#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

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Non-polymers , 7 types, 226 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT / Octaethylene glycol monododecyl ether


Mass: 538.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O9
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: 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
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.33 Å3/Da / Density % sol: 53.8 % / Description: NONE
Crystal growpH: 7.9 / Details: 0.9M AMMONIUM SULFATE, 0.1M TRIS PH 7.9, 5% PEG400

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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: May 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.35→40.86 Å / Num. obs: 67275 / % possible obs: 98.9 % / Observed criterion σ(I): -3.7 / Redundancy: 3.62 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.85
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.7 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.35→39.84 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.149 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22918 3394 5 %RANDOM
Rwork0.19057 ---
obs0.19252 63874 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8127 0 105 214 8446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218372
X-RAY DIFFRACTIONr_bond_other_d0.0010.025739
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9811346
X-RAY DIFFRACTIONr_angle_other_deg0.9193.00113868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60751049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60323.024377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.282151381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8151587
X-RAY DIFFRACTIONr_chiral_restr0.0620.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021661
X-RAY DIFFRACTIONr_nbd_refined0.1820.21643
X-RAY DIFFRACTIONr_nbd_other0.1880.25939
X-RAY DIFFRACTIONr_nbtor_refined0.160.23986
X-RAY DIFFRACTIONr_nbtor_other0.0830.24284
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2241
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.030.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.82225753
X-RAY DIFFRACTIONr_mcbond_other0.12922134
X-RAY DIFFRACTIONr_mcangle_it1.25738435
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.58343294
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.28652911
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
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 213 -
Rwork0.24 4383 -
obs--91.37 %

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