[English] 日本語
Yorodumi
- PDB-7ykc: crystal structure of the Phenylalanine-regulated 3-deoxy-D-arabin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ykc
Titlecrystal structure of the Phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (ARO3) from Saccharomyces cerevisiae
Components3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / DAHP synthase / ARO3
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 / mitochondrion / nucleus / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
Phospho-2-dehydro-3-deoxyheptonate aldolase, phenylalanine-inhibited
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLiu, H. / Luo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903300 China
CitationJournal: Commun Chem / Year: 2023
Title: Mechanistic investigation of a D to N mutation in DAHP synthase that dictates carbon flux into the shikimate pathway in yeast.
Authors: Liu, H. / Xiao, Q. / Wu, X. / Ma, H. / Li, J. / Guo, X. / Liu, Z. / Zhang, Y. / Luo, Y.
History
DepositionJul 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
B: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)82,2602
Polymers82,2602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-33 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.680, 95.561, 105.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase / 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: 41129.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: ARO3, YDR035W, YD9673.07 / Production host: Escherichia coli B (bacteria)
References: UniProt: P14843, 3-deoxy-7-phosphoheptulonate synthase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→105.79 Å / Num. obs: 11363 / % possible obs: 96.6 % / Redundancy: 7 % / Biso Wilson estimate: 128.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Net I/σ(I): 9.6 / Num. measured all: 79559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.567.31.5031660422760.6230.5871.6171.395.9
8.73-105.795.90.05542217110.9960.0240.0627.998.9

-
Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Blu-Icedata collection
Aimlessdata scaling
PHENIXphasing
autoPROCdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 3.3→34.37 Å / SU ML: 0.75 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 1130 9.98 %
Rwork0.252 --
obs0.2562 11322 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5759 0 0 0 5759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135850
X-RAY DIFFRACTIONf_angle_d1.767866
X-RAY DIFFRACTIONf_dihedral_angle_d15.1322256
X-RAY DIFFRACTIONf_chiral_restr0.096866
X-RAY DIFFRACTIONf_plane_restr0.0131034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.450.49391300.39851185X-RAY DIFFRACTION93
3.45-3.630.41311430.36311289X-RAY DIFFRACTION100
3.63-3.860.3891300.34581165X-RAY DIFFRACTION89
3.86-4.160.33591310.34021191X-RAY DIFFRACTION91
4.16-4.570.33171460.28161304X-RAY DIFFRACTION100
4.57-5.230.2381460.25831318X-RAY DIFFRACTION100
5.24-6.590.30561480.26981335X-RAY DIFFRACTION100
6.59-34.370.24761560.17891402X-RAY DIFFRACTION99
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)
12.935-0.3992-1.67895.84620.7633.8043-0.47380.06180.1474-0.2336-0.36070.4731-1.89960.66340.82091.2382-0.2947-0.380.7820.29980.9287-30.1041-32.825-2.8153
21.6675-0.2042-2.31586.0307-5.49538.138-0.4894-0.41260.9320.62360.16910.9206-2.5606-0.8361-0.06561.30380.0951-0.44020.94120.00791.6541-41.6393-24.8568-3.5299
35.05751.05061.65245.9276-0.18945.5627-0.6737-0.09451.2754-1.0051-0.53520.8035-3.56280.72120.81242.8262-0.3571-0.81270.90590.32161.4596-32.1487-17.3842-8.5315
45.3887-0.65960.93654.8005-0.47985.4488-0.80342.2041-0.7095-0.8292-0.0532-0.1935-1.11221.3661.01651.1516-0.23180.01981.44410.06471.022-18.6247-38.0934-16.0567
52.99791.46330.41225.88632.14641.6919-0.00590.31180.99010.9489-0.5328-2.6566-0.44592.46260.26911.3284-0.5635-0.51662.70750.24761.9759-2.1602-29.602811.8897
64.65240.42721.87726.63852.85243.0916-0.1676-0.67581.68910.0835-0.3881-0.7135-1.56590.80440.57181.6699-0.8639-0.34021.83140.19411.4788-14.96-16.50915.1588
71.2895-2.09090.51181.9488-0.17261.42771.83850.2728-0.2024-0.1265-1.0688-1.7293-1.41481.920.00351.7924-1.0745-0.38813.17780.16743.0074.0133-15.215114.5564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 370 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 27 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 303 )
7X-RAY DIFFRACTION7chain 'B' and (resid 304 through 370 )

+
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