[English] 日本語
Yorodumi
- PDB-7kn9: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kn9
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dihydrodipicolinate synthase
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / LYSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSaran, S. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND.
Authors: Saran, S. / Majdi Yazdi, M. / Chung, I. / Sanders, D.A.R.
History
DepositionNov 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,15887
Polymers204,7636
Non-polymers5,39581
Water18,6281034
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,16832
Polymers68,2542
Non-polymers1,91330
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-83 kcal/mol
Surface area21090 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,00429
Polymers68,2542
Non-polymers1,74927
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-24 kcal/mol
Surface area21420 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,98726
Polymers68,2542
Non-polymers1,73324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-30 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.310, 231.390, 199.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 18 or resid 20...
21(chain B and (resid 3 through 17 or (resid 18...
31(chain C and (resid 3 through 17 or (resid 18...
41(chain D and (resid 3 through 17 or (resid 18...
51(chain E and (resid 3 through 17 or (resid 18...
61(chain F and (resid 3 through 17 or (resid 18...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYS(chain A and (resid 3 through 18 or resid 20...AA3 - 1815 - 30
12GLYGLYTHRTHR(chain A and (resid 3 through 18 or resid 20...AA20 - 7332 - 85
13LYSLYSLYSLYS(chain A and (resid 3 through 18 or resid 20...AA7486
14LYSLYSPHEPHE(chain A and (resid 3 through 18 or resid 20...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 18 or resid 20...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 18 or resid 20...AA3 - 29815 - 310
21LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 1715 - 29
22LYSLYSLYSLYS(chain B and (resid 3 through 17 or (resid 18...BB1830
23ASPASPPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB2 - 29814 - 310
24ASPASPPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB2 - 29814 - 310
25ASPASPPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB2 - 29814 - 310
31LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 1715 - 29
32LYSLYSLYSLYS(chain C and (resid 3 through 17 or (resid 18...CC1830
33LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 29815 - 310
36LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 29815 - 310
41LYSLYSPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 1715 - 29
42LYSLYSLYSLYS(chain D and (resid 3 through 17 or (resid 18...DD1830
43LYSLYSPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
51LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 1715 - 29
52LYSLYSLYSLYS(chain E and (resid 3 through 17 or (resid 18...EE1830
53LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
61LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 1715 - 29
62LYSLYSLYSLYS(chain F and (resid 3 through 17 or (resid 18...FF1830
63ASPASPPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF2 - 29814 - 310
64ASPASPPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF2 - 29814 - 310
65ASPASPPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF2 - 29814 - 310

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34127.223 Da / Num. of mol.: 6 / Mutation: E88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: dapA, Cj0806 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

-
Non-polymers , 7 types, 1115 molecules

#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1034 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.5 M Magnesium acetate, 8 % PEG 8000, 0.1 M Sodium acetate (pH 7.4), 60 mM L-Lysine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2019
RadiationMonochromator: Double beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.07→45.83 Å / Num. obs: 119299 / % possible obs: 99.3 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 12.44
Reflection shellResolution: 2.07→2.144 Å / Rmerge(I) obs: 0.5427 / Num. unique obs: 11198 / % possible all: 94.16

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.07→45.83 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 5965 5 %
Rwork0.1766 113317 -
obs0.1782 119282 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.47 Å2 / Biso mean: 26.9556 Å2 / Biso min: 15.21 Å2
Refinement stepCycle: final / Resolution: 2.07→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13594 0 281 1034 14909
Biso mean--36.9 30.47 -
Num. residues----1784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5250X-RAY DIFFRACTION2.39TORSIONAL
12B5250X-RAY DIFFRACTION2.39TORSIONAL
13C5250X-RAY DIFFRACTION2.39TORSIONAL
14D5250X-RAY DIFFRACTION2.39TORSIONAL
15E5250X-RAY DIFFRACTION2.39TORSIONAL
16F5250X-RAY DIFFRACTION2.39TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.07-2.090.32281810.2909343891
2.09-2.120.3041860.2691353794
2.12-2.140.30091930.2491366497
2.14-2.170.25391950.2288370499
2.17-2.20.2581970.21033759100
2.2-2.230.22011980.21113746100
2.23-2.260.22961980.20783759100
2.26-2.30.23711980.19923769100
2.3-2.330.25532000.19263796100
2.33-2.370.21531990.19253795100
2.37-2.410.2481980.1933755100
2.41-2.450.24311970.1853746100
2.45-2.50.21492020.19183822100
2.5-2.550.23891960.18133735100
2.55-2.610.22482000.18113789100
2.61-2.670.20122010.17663822100
2.67-2.740.24011980.18333777100
2.74-2.810.22531990.17843766100
2.81-2.890.20681990.18513787100
2.89-2.990.2452000.18213792100
2.99-3.090.20572010.1743826100
3.09-3.220.20591990.17753789100
3.22-3.360.20222000.18443799100
3.36-3.540.21842020.17893833100
3.54-3.760.16542010.16193827100
3.76-4.050.18632020.15143833100
4.05-4.460.16712020.14523838100
4.46-5.10.17282040.14483873100
5.1-6.430.1882060.17333904100
6.43-100.16392130.14824037100

+
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