[English] 日本語
Yorodumi
- PDB-2w19: Non-covalent complex between dahp synthase and chorismate mutase ... -

+
Open data


ID or keywords:

Loading...

-
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 / cytoplasm / cytosol
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 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, subunit A / Chorismate mutase domain superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more