[English] 日本語
Yorodumi
- PDB-6ub9: Crystal structure of tryptophan synthase from M. tuberculosis - A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ub9
TitleCrystal structure of tryptophan synthase from M. tuberculosis - AMINOACRYLATE- AND BRD6309-BOUND FORM
Components(Tryptophan synthase ...) x 2
KeywordsLyase/Lyase Inhibitor / PLP / heterotetramer / amino acid biosynthesis / substrate channeling / allostery / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Lyase-Lyase Inhibitor complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme ...Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / FORMIC ACID / Chem-H9V / MALONIC ACID / Chem-P1T / TRIETHYLENE GLYCOL / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.783 Å
AuthorsChang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Satchell, K. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support Canada, 1items
OrganizationGrant numberCountry
Structure-guided Drug Discovery Coalition Canada
CitationJournal: To be Published
Title: Crystal structure of tryptophan synthase from M. tuberculosis - AMINOACRYLATE- AND BRD6309-BOUND FORM
Authors: Chang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Satchell, K. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
SupersessionOct 30, 2019ID: 6DUA
Revision 1.1Oct 30, 2019Group: Advisory / Data collection / Category: pdbx_database_PDB_obs_spr
Revision 1.2Oct 11, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,44044
Polymers287,6568
Non-polymers4,78436
Water3,099172
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,18922
Polymers143,8284
Non-polymers2,36118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-117 kcal/mol
Surface area41510 Å2
MethodPISA
2
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,25022
Polymers143,8284
Non-polymers2,42218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-121 kcal/mol
Surface area41400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.373, 159.619, 164.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Tryptophan synthase ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Tryptophan synthase alpha chain


Mass: 28579.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpA, Rv1613, MTCY01B2.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain


Mass: 43334.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX9, tryptophan synthase

-
Non-polymers , 9 types, 208 molecules

#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical
ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O7P
#6: Chemical
ChemComp-H9V / (2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile


Mass: 336.739 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H12ClF3N2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% TACSIMATE, 20% PEG3350, 5% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.783→30 Å / Num. obs: 84351 / % possible obs: 94.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.086 / Rrim(I) all: 0.219 / Χ2: 0.935 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.855.31.29640720.5890.5791.4250.74892.3
2.85-2.95.41.21740790.6140.5391.3350.79692.2
2.9-2.965.51.09640550.6630.4831.2010.77592.2
2.96-3.025.70.97840910.7390.4281.070.77692.1
3.02-3.085.70.84340580.7880.3680.9220.80192
3.08-3.155.80.68340750.8290.2970.7470.82992.2
3.15-3.235.90.56740400.8720.2440.6190.81991.5
3.23-3.3260.47940560.9020.2060.5230.85291.5
3.32-3.426.10.38540450.920.1650.420.88191.7
3.42-3.536.20.33840440.9410.1440.3680.89291.3
3.53-3.656.30.26240600.9650.110.2850.91791.4
3.65-3.86.30.2240670.9770.0920.2390.92391.7
3.8-3.976.30.18241510.9860.0760.1970.96592.8
3.97-4.186.20.15742590.9890.0650.170.96695.7
4.18-4.446.20.12643960.9930.0530.1371.08698.4
4.44-4.786.30.10544710.9950.0440.1141.11499.8
4.78-5.266.30.10845020.9950.0450.1171.03399.9
5.26-6.026.30.11645190.9940.0490.1260.897100
6.02-7.566.40.0845750.9960.0340.0870.93499.8
7.56-306.20.03947360.9950.0170.0431.45699.8

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TCJ

5tcj


Resolution: 2.783→29.893 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2097 1675 1.99 %
Rwork0.1687 --
obs0.1695 84265 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.03 Å2 / Biso mean: 43.1215 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 2.783→29.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19122 0 288 172 19582
Biso mean--49.79 32.77 -
Num. residues----2598
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7833-2.86520.30611380.2729606583
2.8652-2.95760.31791350.2655667792
2.9576-3.06320.28411290.2517670692
3.0632-3.18570.25531510.225665392
3.1857-3.33050.27651440.2076669191
3.3305-3.50580.25161360.1937663891
3.5058-3.72510.20311330.1627667791
3.7251-4.01210.18421470.151680993
4.0121-4.41470.1621460.1392715297
4.4147-5.05080.1911260.12967388100
5.0508-6.35340.19371620.15377465100
6.3534-29.8930.14541280.13227669100
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)
10.6238-0.0512-0.38510.984-0.17451.8194-0.05340.0665-0.1179-0.1718-0.0698-0.00080.26360.01010.11530.2569-0.00090.01870.2108-0.03360.247731.6617-24.2556-12.7953
22.22770.09920.34421.7491-0.68942.00910.1323-0.1015-0.2196-0.02320.00960.5220.0807-0.1739-0.13290.23720.03840.02790.2885-0.04630.4736-18.111713.561414.7069
30.8105-0.1164-0.45771.02530.20921.29160.0431-0.0330.0247-0.0667-0.040.0957-0.0853-0.0329-0.00580.2157-0.0052-0.02120.2542-0.01090.252516.36593.7132.6742
42.704-0.66850.60721.117-0.00782.46780.08640.365-0.0738-0.0945-0.1184-0.29610.11790.24150.0350.24380.0080.06140.35590.04380.463586.4661-12.797316.7208
50.71420.1008-0.39150.97130.10241.19740.0438-0.0508-0.0180.0243-0.0252-0.1022-0.09260.0937-0.02250.21860.0003-0.00870.27470.0310.246451.3885-5.01828.5037
61.493-0.80160.26052.6723-0.63612.0479-0.0193-0.34870.02740.8740.02810.3146-0.4428-0.2424-0.00550.6033-0.08640.16680.3826-0.0090.40379.3326-26.804578.2186
70.77230.1812-0.39470.71360.09381.36580.02-0.0455-0.03090.0265-0.0705-0.01040.0743-0.11120.05250.2057-0.00590.00130.27580.02440.272224.3111-21.839443.8359
81.76180.72320.14831.1660.56711.7563-0.65460.7152-0.2222-1.00080.429-0.33610.30890.20770.17231.0535-0.18680.24310.608-0.08750.476841.5056-35.9345-47.2182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'F' and resid 8 through 407)F8 - 407
2X-RAY DIFFRACTION2(chain 'G' and resid 9 through 267)G9 - 267
3X-RAY DIFFRACTION3(chain 'H' and resid 5 through 407)H5 - 407
4X-RAY DIFFRACTION4(chain 'A' and resid 8 through 267)A8 - 267
5X-RAY DIFFRACTION5(chain 'B' and resid 5 through 408)B5 - 408
6X-RAY DIFFRACTION6(chain 'C' and resid 8 through 266)C8 - 266
7X-RAY DIFFRACTION7(chain 'D' and resid 9 through 407)D9 - 407
8X-RAY DIFFRACTION8(chain 'E' and resid 9 through 266)E9 - 266

+
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