[English] 日本語
Yorodumi
- PDB-6x0c: Tryptophan Synthase mutant beta-Q114A in complex with Cesium ion ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x0c
TitleTryptophan Synthase mutant beta-Q114A in complex with Cesium ion at the metal coordination site and aminoacrylate and benzimidazole at the enzyme beta site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / Protein complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytosol / cytoplasm
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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-0JO / BENZIMIDAZOLE / : / DI(HYDROXYETHYL)ETHER / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01GM097569-06A1 United States
CitationJournal: To be Published
Title: External aldimine form of Tryptophan Synthase mutant beta-Q114A in complex with Cesium ion at the metal coordination site and benzimidazole at the enzyme beta site.
Authors: Hilario, E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,40921
Polymers71,5612
Non-polymers1,84819
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, S-200 at 277K
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-66 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.133, 59.336, 67.419
Angle α, β, γ (deg.)90.000, 95.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1097-

HOH

-
Components

-
Tryptophan synthase ... , 2 types, 2 molecules AB

#1: Protein Tryptophan synthase alpha chain


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42861.828 Da / Num. of mol.: 1 / Mutation: Q114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: pEBA-10 / Details (production host): beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

-
Non-polymers , 8 types, 611 molecules

#3: Chemical ChemComp-BZI / BENZIMIDAZOLE / Benzimidazole


Mass: 118.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.62 Å3/Da / Density % sol: 53.14 % / Description: Large plate-like crystal (200x100x100 microns)
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
PH range: 7.6-8.0 / Temp details: constant

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. obs: 127033 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.03 / Rrim(I) all: 0.111 / Rsym value: 0.104 / Net I/av σ(I): 3 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.45-1.53131.1030.6240545185070.3231.1731.1033.899.9
1.53-1.6213.30.6151.1232526174460.1780.6540.6155.6100
1.62-1.7313.40.3721.8220768164370.1080.3960.3728100
1.73-1.8713.40.2262.9204693153240.0660.2410.22610.799.9
1.87-2.0513.50.1564.1189643140870.0450.1670.15613.8100
2.05-2.2913.20.1215.1168793127580.0350.1290.12117.599.9
2.29-2.6513.50.1075.6152188112990.0310.1140.10720.6100
2.65-3.2413.10.15.812543095610.0290.1070.124.7100
3.24-4.5913.10.0856.79780274430.0250.0910.08532.799.9
4.59-39.39112.90.0776.95369341710.0220.0820.07734.199.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.78 Å39.39 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALA3.3.22data scaling
PHASER2.8.3phasing
PARROT1.0.4phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VFD

6vfd


Resolution: 1.45→39.39 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.189 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 6260 4.9 %RANDOM
Rwork0.1636 ---
obs0.1656 120752 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.87 Å2 / Biso mean: 27.857 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.35 Å2
2---1.05 Å20 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 1.45→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 100 608 5602
Biso mean--38.13 39.96 -
Num. residues----647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135282
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174951
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6387164
X-RAY DIFFRACTIONr_angle_other_deg1.4851.5711490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65222.364258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53315872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0151532
X-RAY DIFFRACTIONr_chiral_restr0.0810.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026080
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021082
X-RAY DIFFRACTIONr_rigid_bond_restr3.79535261
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 432 -
Rwork0.273 8403 -
all-8835 -
obs--94.48 %
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)
15.1815-1.49540.38732.1409-0.07181.7487-0.0358-0.06930.10660.05990.0301-0.1843-0.01090.38650.00580.1489-0.0532-0.01070.10930.01290.194751.73312.19511.651
22.02170.8863-0.15082.711-0.41780.95570.1175-0.08020.23960.1514-0.0840.0895-0.20010.0105-0.03350.0881-0.01340.00370.0058-0.00110.114737.82510.1818.648
33.2971-1.08740.40664.2695-0.96894.0543-0.0385-0.4349-0.15550.51140.0536-0.12570.20290.2934-0.01510.1574-0.0114-0.05810.15810.03230.224649.357-4.83419.582
41.1124-0.14230.24054.58881.55533.0941-0.0948-0.2102-0.04390.42930.09840.1325-0.06140.1305-0.00360.1547-0.0308-0.05220.1588-0.01010.196451.6187.05323.024
54.5104-2.34390.53987.0111-1.31751.7838-0.0197-0.3446-0.09960.24270.03170.2496-0.0467-0.0042-0.01190.24020.01130.00770.1433-0.04380.251737.59524.20222.493
65.6448-4.25311.13835.0929-0.88811.40550.04430.02550.35820.0679-0.0642-0.1559-0.19060.14870.01990.2198-0.0058-0.04640.1325-0.02030.240749.17924.69220.07
71.95640.2172-0.9480.5653-1.11992.80180.0457-0.0902-0.30410.0243-0.12-0.10240.06320.36060.07430.03470.0227-0.06530.0528-0.02050.151327.779-12.70720.072
82.2407-0.30510.8710.6211-0.44172.568-0.0573-0.2698-0.09910.00920.034-0.05310.1236-0.24790.02330.0405-0.0057-0.01380.04280.01160.02980.781-17.53327.5
91.85990.34030.76930.55580.62662.1010.0326-0.24710.12840.0462-0.0183-0.0759-0.14270.1271-0.01420.0752-0.019-0.01540.0824-0.00560.045710.067-8.71630.431
101.03320.04550.56162.9544-1.84343.68810.18210.10340.3478-0.01470.02350.0974-0.6540.0855-0.20560.4085-0.02830.09310.1809-0.01770.274813.3556.96132.398
112.7587-0.0388-0.35650.1443-0.1911.53040.0521-0.13180.09260.0503-0.054-0.0541-0.06530.12650.00190.0501-0.0077-0.02680.03220.0090.027812.07-11.37521.032
121.38540.0691-0.07054.8313-0.6971.3565-0.00230.11680.0665-0.1968-0.036-0.1465-0.040.03120.03830.03440.0063-0.01110.02160.00680.02135.834-4.6957.6
133.6438-0.5869-0.01515.9081-1.98660.68640.08720.09220.50680.0429-0.02260.1191-0.04290.0069-0.06470.0943-0.0184-0.01620.05040.03480.109720.762.5078.354
142.4045-0.7902-0.35180.4309-0.29881.06130.024-0.03060.29270.0710.0086-0.1004-0.17750.0335-0.03260.0519-0.0024-0.01880.0139-0.00160.056910.959-4.28811.45
151.93240.5824-0.14080.9216-0.11541.68430.0159-0.04530.13720.0702-0.01150.1103-0.1791-0.2316-0.00440.04450.0205-0.01360.0347-0.00150.0344-6.623-2.77114.067
162.17640.61070.8582.05820.37133.4308-0.028-0.11210.42640.2141-0.01030.2224-0.475-0.17660.03830.10230.01780.0250.04940.00090.1018-6.539-0.93418.494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 159
3X-RAY DIFFRACTION3A160 - 202
4X-RAY DIFFRACTION4A203 - 234
5X-RAY DIFFRACTION5A235 - 247
6X-RAY DIFFRACTION6A248 - 268
7X-RAY DIFFRACTION7B2 - 37
8X-RAY DIFFRACTION8B38 - 70
9X-RAY DIFFRACTION9B71 - 126
10X-RAY DIFFRACTION10B127 - 165
11X-RAY DIFFRACTION11B166 - 244
12X-RAY DIFFRACTION12B245 - 273
13X-RAY DIFFRACTION13B274 - 295
14X-RAY DIFFRACTION14B296 - 322
15X-RAY DIFFRACTION15B323 - 365
16X-RAY DIFFRACTION16B366 - 395

+
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