[English] 日本語
Yorodumi
- PDB-7ly8: The internal aldimine form of the wild-type Salmonella Typhimuriu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ly8
TitleThe internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the enzyme alpha-site, a single F6F molecule at the enzyme beta-site, and sodium ion at the metal coordination site at 1.55 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / inhibitor / internal aldimine / LYASE / LYASE-LYASE INHIBITOR 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-F6F / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J.
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: The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor ...Title: The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the enzyme alpha-site, a single F6F molecule at the enzyme beta-site, and sodium ion at the metal coordination site at 1.55 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionMar 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)73,40717
Polymers71,6182
Non-polymers1,78915
Water10,917606
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tryptophan Synthase complex (alpha2-beta2). TS is a tetramer in solution and composed of two alpha-chains and two beta-chains.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-26 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.645, 58.800, 67.205
Angle α, β, γ (deg.)90.000, 95.130, 90.000
Int Tables number5
Space group name H-MC121

-
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: 42918.879 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: trpB / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

-
Non-polymers , 7 types, 621 molecules

#3: Chemical ChemComp-F6F / 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZOYL)-2-AMINO-1-ETHYLPHOSPHATE, F6


Mass: 329.166 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H11F3NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.6 Å3/Da / Density % sol: 52.71 % / Description: large plate-like crystal
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: 7.60-8.00 / Temp details: constant

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 5, 2021 / Details: VariMax HighFlux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.549→91.455 Å / Num. obs: 99219 / % possible obs: 95.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.04 / Rrim(I) all: 0.071 / Rsym value: 0.051 / Net I/av σ(I): 7.6 / Net I/σ(I): 8.6
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
1.55-1.631.70.2992.418516109800.3120.4760.2991.673
1.63-1.732.80.3092.438955140460.2190.3820.3092.898.8
1.73-1.852.90.2233.238443133480.1540.2690.223499.6
1.85-22.90.1454.836178124440.1030.180.145699.8
2-2.192.90.1026.333973115230.0710.1250.1028.699.9
2.19-2.4530.074831094104450.0530.0920.07410.999.9
2.45-2.8330.05610.32763292130.0390.070.05613.499.9
2.83-3.4730.04213.52375078010.0310.0540.04217.399.9
3.47-4.93.10.0312.71858560680.0220.040.0321.199.7
4.9-36.8230.02116.51018133510.0180.0320.02120.498.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.504
Highest resolutionLowest resolution
Rotation36.82 Å1.81 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 99152
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.4-10029.50.933670
5.94-8.4370.9311211
4.85-5.9433.10.9071564
4.2-4.8522.50.9381843
3.76-4.222.20.9362089
3.43-3.7620.80.9352312
3.18-3.4321.80.9222521
2.97-3.1822.70.9152679
2.8-2.9721.70.9192843
2.66-2.8210.9163024
2.53-2.6620.70.9183185
2.43-2.5320.70.9143299
2.33-2.4319.50.9213435
2.25-2.3318.60.9193586
2.17-2.2518.90.9243695
2.1-2.1718.50.9333830
2.04-2.118.20.9323970
1.98-2.0419.30.934065
1.93-1.9818.70.9334169
1.88-1.9320.80.9164297
1.83-1.8822.30.914393
1.79-1.8323.70.9084478
1.75-1.7923.70.9064594
1.71-1.7524.30.9044665
1.68-1.7125.40.94745
1.65-1.6827.20.8844869
1.62-1.6529.30.8684673
1.59-1.6231.60.8453986
1.55-1.5936.60.8114462

-
Processing

Software
NameVersionClassification
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.55→36.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.317 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0789 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4999 5 %RANDOM
Rwork0.1728 ---
obs0.1738 94154 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.13 Å2 / Biso mean: 21.956 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.26 Å2
2--0.14 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.55→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 107 627 5591
Biso mean--29.17 32.69 -
Num. residues----646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125253
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.6347144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57922.385260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90115842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9741532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024097
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 236 -
Rwork0.311 4535 -
all-4771 -
obs--62.39 %
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)
10.46780.25380.33680.35530.16770.75080.0042-0.09240.154-0.0036-0.02940.0304-0.1277-0.04290.02520.0358-0.01270.02260.0371-0.03060.085138.63317.60211.702
20.82770.3822-0.12770.6502-0.27230.15520.0515-0.0444-0.0377-0.0392-0.0599-0.0148-0.02230.03440.00850.0604-0.01280.00410.06190.0020.030639.1192.3437.023
30.30960.16980.16691.98850.82140.49870.0747-0.1748-0.07710.0364-0.0528-0.07880.0057-0.0343-0.02180.0265-0.0409-0.0310.14010.03460.0448.2914.56620.92
44.573-3.65312.52616.2324-0.77131.8762-0.3116-0.04060.18970.10370.1648-0.0765-0.26870.05570.14680.1431-0.0911-0.04230.09160.01190.019950.4623.9720.223
50.29710.030.02060.0036-0.01040.3617-0.0213-0.0376-0.025-0.0012-0.0059-0.00480.03050.01520.02720.04730.0052-0.01230.05160.01050.031412.184-14.17724.775
61.104-0.1096-0.59920.7791-0.42460.6830.20720.03530.18460.0418-0.06530.0632-0.0890.0575-0.14190.10110.00910.02810.07590.0090.043814.8053.02233.106
70.17620.1026-0.11130.13340.06370.313-0.0051-0.0378-0.0097-0.00650.0024-0.00220.0290.07350.00270.04820.0012-0.01780.0740.00610.034316.093-9.76823.979
80.27880.0567-0.08030.0239-0.00390.13610.00970.03340.0340.0072-0.01340.0040.01410.01270.00370.0492-0.0046-0.00830.05630.00530.04269.52-4.20510.57
90.6025-0.1402-0.23630.04390.0580.5047-0.00320.0190.0465-0.01620.013-0.0027-0.00850.0023-0.00980.047-0.0049-0.01190.04880.00720.03432.409-4.1712.569
100.17980.1314-0.05980.16840.19730.86370.04250.0160.01570.00480.0193-0.0087-0.0658-0.0529-0.06190.05440.00330.00110.0773-0.00120.0268-6.477-2.87916.373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 91
2X-RAY DIFFRACTION2A92 - 159
3X-RAY DIFFRACTION3A160 - 247
4X-RAY DIFFRACTION4A248 - 268
5X-RAY DIFFRACTION5B2 - 100
6X-RAY DIFFRACTION6B101 - 165
7X-RAY DIFFRACTION7B166 - 220
8X-RAY DIFFRACTION8B221 - 301
9X-RAY DIFFRACTION9B302 - 343
10X-RAY DIFFRACTION10B344 - 394

+
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://pdbjlc1.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