[English] 日本語
Yorodumi
- PDB-2g5f: The structure of MbtI from Mycobacterium Tuberculosis, the first ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g5f
TitleThe structure of MbtI from Mycobacterium Tuberculosis, the first enzyme in the synthesis of Mycobactin, reveals it to be a salicylate synthase
ComponentsCOG0147: Anthranilate/para-aminobenzoate synthases component I
KeywordsBIOSYNTHETIC PROTEIN / Beta Sandwhich / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / iron acquisition from host / isochorismate synthase / oxo-acid-lyase activity / isochorismate synthase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase ...isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / iron acquisition from host / isochorismate synthase / oxo-acid-lyase activity / isochorismate synthase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity / L-tryptophan biosynthetic process / magnesium ion binding / plasma membrane
Similarity search - Function
Salicylate synthase / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / PYRUVIC ACID / Salicylate synthase / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHarrison, A.J. / Lott, J.S. / Yu, M. / Ramsay, R. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Bacteriol. / Year: 2006
Title: The Structure of MbtI from Mycobacterium tuberculosis, the First Enzyme in the Biosynthesis of the Siderophore Mycobactin, Reveals It To Be a Salicylate Synthase
Authors: Harrison, A.J. / Gardenborg, T. / Yu, M. / Middleditch, M. / Ramsay, R.J. / Baker, E.N. / Lott, J.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COG0147: Anthranilate/para-aminobenzoate synthases component I
B: COG0147: Anthranilate/para-aminobenzoate synthases component I
C: COG0147: Anthranilate/para-aminobenzoate synthases component I
D: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,12216
Polymers195,1174
Non-polymers1,00512
Water17,889993
1
A: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0284
Polymers48,7791
Non-polymers2493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9593
Polymers48,7791
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1025
Polymers48,7791
Non-polymers3224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: COG0147: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0324
Polymers48,7791
Non-polymers2533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.820, 163.370, 194.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe molecule runs as a monomer on size exclusion chromatography.

-
Components

#1: Protein
COG0147: Anthranilate/para-aminobenzoate synthases component I / MbtI Salicylate synthase


Mass: 48779.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MbtI / Plasmid: pEt42a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) pRI/L / References: UniProt: Q7D785, UniProt: P9WFX1*PLUS
#2: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 993 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 316 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% PEG 4000, 0.2M Immadazole/malate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 316K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9393
SYNCHROTRONALS 5.0.220.9796, 0.9797
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 4, 2003
ADSC QUANTUM 3152CCDJan 10, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
20.97961
30.97971
ReflectionResolution: 1.8→50 Å / Num. all: 154253 / Num. obs: 154236 / % possible obs: 26 % / Observed criterion σ(F): 23.06 / Observed criterion σ(I): 4.75
Reflection shellResolution: 1.8→1.9 Å / % possible all: 97.6

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / FOM work R set: 0.846 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 15321 9.9 %Random
Rwork0.205 ---
all0.208 153352 --
obs0.208 153352 99.4 %-
Solvent computationBsol: 43.448 Å2
Displacement parametersBiso mean: 23.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.133 Å20 Å20 Å2
2---0.294 Å20 Å2
3---0.427 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13110 0 68 993 14171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcangle_it1.5
X-RAY DIFFRACTIONc_mcbond_it2
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8-1.810.3193080.28926032911
1.81-1.820.3142820.2727022984
1.82-1.840.3013130.27626492962
1.84-1.850.2922910.26426572948
1.85-1.860.2932810.25226682949
1.86-1.880.2743310.24526472978
1.88-1.890.2953240.24227103034
1.89-1.910.2692850.24127393024
1.91-1.920.2663030.23627093012
1.92-1.940.283080.22526712979
1.94-1.960.2593010.22527193020
1.96-1.970.2562870.21327873074
1.97-1.990.2423090.21627683077
1.99-2.010.2572770.21527062983
2.01-2.030.2612990.21427603059
2.03-2.050.2593010.2127533054
2.05-2.070.2443150.20227763091
2.07-2.090.2612910.21227353026
2.09-2.110.252970.21127383035
2.11-2.130.2492960.21427393035
2.13-2.160.2342890.19928203109
2.16-2.180.263190.20227073026
2.18-2.210.2522930.20727613054
2.21-2.240.2453200.20527803100
2.24-2.270.2592960.20627543050
2.27-2.30.2532930.20427473040
2.3-2.330.2453040.20127813085
2.33-2.370.2453120.20227693081
2.37-2.40.2482970.19727413038
2.4-2.440.2523140.20627793093
2.44-2.490.2423230.19927433066
2.49-2.530.2572970.21127633060
2.53-2.580.2513160.21327693085
2.58-2.630.2473200.2127513071
2.63-2.690.2552940.21528073101
2.69-2.750.2623150.21627593074
2.75-2.820.2383320.20827503082
2.82-2.90.2543210.21727833104
2.9-2.980.2422930.20927693062
2.98-3.080.253130.21127883101
3.08-3.190.2432940.21528003094
3.19-3.320.2442960.20328053101
3.32-3.470.2313060.18828323138
3.47-3.650.23310.18827823113
3.65-3.880.2153070.18528133120
3.88-4.180.1983170.17528113128
4.18-4.60.1973200.1728423162
4.6-5.260.1973060.18628813187
5.26-6.630.2773240.24928993223
6.63-500.010.2223600.19130093369
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4glyparam.paramion.top
X-RAY DIFFRACTION5cis_peptide.paramglytopology.top
X-RAY DIFFRACTION6imdparam.paramimdtopology.top
X-RAY DIFFRACTION7imdparam.paramimdtopology.top

+
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://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