[English] 日本語
Yorodumi
- PDB-6agm: Molecular basis for feedback inhibition of tyrosine-regulated 3-d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6agm
TitleMolecular basis for feedback inhibition of tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
KeywordsBIOSYNTHETIC PROTEIN / 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) / Escherichia coli / aromatic amino acid biosynthesis / feedback inhibition / allosteric regulation.
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / identical protein binding / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCui, D. / Qi, J. / Wen, T.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Molecular basis for feedback inhibition of tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli.
Authors: Cui, D. / Deng, A. / Bai, H. / Yang, Z. / Liang, Y. / Liu, Z. / Qiu, Q. / Wang, L. / Liu, S. / Zhang, Y. / Shi, Y. / Qi, J. / Wen, T.
History
DepositionAug 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
C: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
D: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8248
Polymers155,0994
Non-polymers7254
Water5,080282
1
A: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules

C: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9124
Polymers77,5502
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_547-x,y-1/2,-z+21
Buried area6140 Å2
ΔGint-12 kcal/mol
Surface area24020 Å2
MethodPISA
2
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules

D: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9124
Polymers77,5502
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y+1/2,-z+31
Buried area6230 Å2
ΔGint-13 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.189, 133.859, 87.670
Angle α, β, γ (deg.)90.00, 91.23, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3- ...3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3-deoxyheptonate aldolase


Mass: 38774.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: aroF, b2601, JW2582 / Production host: Escherichia coli (E. coli)
References: UniProt: P00888, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical
ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 16% PEG 4000, 10% 2-propanol, 0.1 M sodium citrate, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 82353 / % possible obs: 97 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rpim(I) all: 0.036 / Rsym value: 0.088 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 6902 / CC1/2: 0.651 / Rpim(I) all: 0.368 / Rsym value: 0.788

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QR7

1qr7


Resolution: 2→38.207 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.62
RfactorNum. reflection% reflection
Rfree0.2288 4111 5 %
Rwork0.1933 --
obs0.195 82301 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→38.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10232 0 0 282 10514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910408
X-RAY DIFFRACTIONf_angle_d0.73714104
X-RAY DIFFRACTIONf_dihedral_angle_d25.4793900
X-RAY DIFFRACTIONf_chiral_restr0.0441588
X-RAY DIFFRACTIONf_plane_restr0.0051880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9937-2.01720.3577950.29952053X-RAY DIFFRACTION74
2.0172-2.04180.3241130.28872300X-RAY DIFFRACTION82
2.0418-2.06760.29631170.27752382X-RAY DIFFRACTION86
2.0676-2.09480.32151340.27362494X-RAY DIFFRACTION89
2.0948-2.12350.29261480.27312537X-RAY DIFFRACTION92
2.1235-2.15390.33231610.27692590X-RAY DIFFRACTION95
2.1539-2.1860.31091230.26272697X-RAY DIFFRACTION97
2.186-2.22020.26511490.25032712X-RAY DIFFRACTION98
2.2202-2.25660.2791390.2422796X-RAY DIFFRACTION99
2.2566-2.29550.2591450.2422736X-RAY DIFFRACTION100
2.2955-2.33720.3021280.23832779X-RAY DIFFRACTION100
2.3372-2.38220.26211250.23262800X-RAY DIFFRACTION100
2.3822-2.43080.24681530.22922790X-RAY DIFFRACTION100
2.4308-2.48360.30111670.23322734X-RAY DIFFRACTION100
2.4836-2.54140.29821640.22632755X-RAY DIFFRACTION100
2.5414-2.60490.26691630.22872786X-RAY DIFFRACTION100
2.6049-2.67530.25431390.22712767X-RAY DIFFRACTION100
2.6753-2.7540.26291460.22542765X-RAY DIFFRACTION100
2.754-2.84290.2411480.2332804X-RAY DIFFRACTION100
2.8429-2.94450.27311470.23352747X-RAY DIFFRACTION100
2.9445-3.06230.24971300.22562818X-RAY DIFFRACTION100
3.0623-3.20160.26881310.21892808X-RAY DIFFRACTION100
3.2016-3.37030.25511520.20642777X-RAY DIFFRACTION100
3.3703-3.58130.23521500.1872768X-RAY DIFFRACTION100
3.5813-3.85760.21881580.17962766X-RAY DIFFRACTION100
3.8576-4.24540.20521560.15382782X-RAY DIFFRACTION100
4.2454-4.85860.16661510.152807X-RAY DIFFRACTION100
4.8586-6.11730.2071380.17012798X-RAY DIFFRACTION100
6.1173-38.2140.16651410.15052842X-RAY DIFFRACTION100
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71330.0898-0.25790.82250.16980.74420.03160.05560.1238-0.0872-0.0110.0596-0.0412-0.02470.271-0.0059-0.02160.2519-0.00530.25651.328617.7391102.7374
21.54470.3719-0.0950.6576-0.06770.94670.035-0.03060.070.09320.02170.06410.0864-0.08780.35020.02260.01550.3380.0130.3378-25.26355.7904119.2073
31.0755-0.33690.17671.9543-0.30920.89940.02690.0417-0.0669-0.1441-0.0116-0.04890.0986-0.01450.2992-0.00290.02230.2949-0.00330.3088-18.999253.150674.6699
40.75070.36210.09791.2887-0.25550.6112-0.02810.03410.04230.15820.0421-0.0129-0.1585-0.04190.38970.0326-0.00630.37830.00220.33425.942720.3068147.6963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 350 )
2X-RAY DIFFRACTION2chain 'B' and (resid 10 through 350 )
3X-RAY DIFFRACTION3chain 'C' and (resid 10 through 350 )
4X-RAY DIFFRACTION4chain 'D' and (resid 10 through 350 )

+
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