[English] 日本語
Yorodumi
- PDB-7kg2: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kg2
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site and L-histidine bound at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / DIHYDRODIPICOLINATE SYNTHASE
Function / homology
Function and homology information


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / 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 / HISTIDINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSaran, S. / Majdi Yazdi, M. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To be Published
Title: Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site
Authors: Majdi Yazdi, M.M. / Saran, S. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionOct 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 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)211,50593
Polymers205,0586
Non-polymers6,44887
Water13,709761
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,15429
Polymers68,3532
Non-polymers1,80227
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint1 kcal/mol
Surface area23210 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,97336
Polymers68,3532
Non-polymers2,62034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-0 kcal/mol
Surface area21980 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,37928
Polymers68,3532
Non-polymers2,02626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-13 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.780, 230.740, 202.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-491-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 73 or (resid 74...
21(chain B and (resid 3 through 145 or resid 147...
31(chain C and (resid 3 through 73 or (resid 74...
41(chain D and (resid 3 through 73 or (resid 74...
51(chain E and (resid 3 through 73 or (resid 74...
61(chain F and (resid 3 through 73 or (resid 74...

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
11LYSLYSTHRTHR(chain A and (resid 3 through 73 or (resid 74...AA3 - 7315 - 85
12LYSLYSLYSLYS(chain A and (resid 3 through 73 or (resid 74...AA7486
13LYSLYSPHEPHE(chain A and (resid 3 through 73 or (resid 74...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 73 or (resid 74...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 73 or (resid 74...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 73 or (resid 74...AA3 - 29815 - 310
21LYSLYSCYSCYS(chain B and (resid 3 through 145 or resid 147...BB3 - 14515 - 157
22ILEILEGLUGLU(chain B and (resid 3 through 145 or resid 147...BB147 - 160159 - 172
23ILEILEILEILE(chain B and (resid 3 through 145 or resid 147...BB162 - 218174 - 230
24ALAALALEULEU(chain B and (resid 3 through 145 or resid 147...BB220 - 226232 - 238
25GLUGLUPHEPHE(chain B and (resid 3 through 145 or resid 147...BB228 - 298240 - 310
31LYSLYSTHRTHR(chain C and (resid 3 through 73 or (resid 74...CC3 - 7315 - 85
32LYSLYSLYSLYS(chain C and (resid 3 through 73 or (resid 74...CC7486
33LYSLYSPHEPHE(chain C and (resid 3 through 73 or (resid 74...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 73 or (resid 74...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 73 or (resid 74...CC3 - 29815 - 310
36LYSLYSPHEPHE(chain C and (resid 3 through 73 or (resid 74...CC3 - 29815 - 310
37LYSLYSPHEPHE(chain C and (resid 3 through 73 or (resid 74...CC3 - 29815 - 310
41LYSLYSTHRTHR(chain D and (resid 3 through 73 or (resid 74...DD3 - 7315 - 85
42LYSLYSLYSLYS(chain D and (resid 3 through 73 or (resid 74...DD7486
43LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
46LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
47LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
51LYSLYSTHRTHR(chain E and (resid 3 through 73 or (resid 74...EE3 - 7315 - 85
52LYSLYSLYSLYS(chain E and (resid 3 through 73 or (resid 74...EE7486
53LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
57LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
61LYSLYSTHRTHR(chain F and (resid 3 through 73 or (resid 74...FF3 - 7315 - 85
62LYSLYSLYSLYS(chain F and (resid 3 through 73 or (resid 74...FF7486
63ASPASPPHEPHE(chain F and (resid 3 through 73 or (resid 74...FF2 - 29814 - 310
64ASPASPPHEPHE(chain F and (resid 3 through 73 or (resid 74...FF2 - 29814 - 310
65ASPASPPHEPHE(chain F and (resid 3 through 73 or (resid 74...FF2 - 29814 - 310
66ASPASPPHEPHE(chain F and (resid 3 through 73 or (resid 74...FF2 - 29814 - 310
67ASPASPPHEPHE(chain F and (resid 3 through 73 or (resid 74...FF2 - 29814 - 310

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

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


Mass: 34176.293 Da / Num. of mol.: 6 / Mutation: H59K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: dapA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2U0QMK8, 4-hydroxy-tetrahydrodipicolinate synthase

-
Non-polymers , 8 types, 848 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10N3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / 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: 48.99 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 10 % PEG8000, 0.1 M Sodium acetate (pH 7.4)

-
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 S 6M / Detector: PIXEL / Date: Oct 17, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→49.63 Å / Num. obs: 156110 / % possible obs: 98.8 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 11.08
Reflection shellResolution: 1.89→1.958 Å / Rmerge(I) obs: 0.8071 / Num. unique obs: 15438 / % possible all: 98.75

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 1.89→49.63 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 7806 5 %
Rwork0.1695 148280 -
obs0.1714 156086 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.07 Å2 / Biso mean: 29.9293 Å2 / Biso min: 14.57 Å2
Refinement stepCycle: final / Resolution: 1.89→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13675 0 354 761 14790
Biso mean--41.07 35 -
Num. residues----1783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5220X-RAY DIFFRACTION5.433TORSIONAL
12B5220X-RAY DIFFRACTION5.433TORSIONAL
13C5220X-RAY DIFFRACTION5.433TORSIONAL
14D5220X-RAY DIFFRACTION5.433TORSIONAL
15E5220X-RAY DIFFRACTION5.433TORSIONAL
16F5220X-RAY DIFFRACTION5.433TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.910.34442560.3224854511099
1.91-1.930.29272580.28124899515799
1.93-1.960.3022580.25924910516899
1.96-1.980.30442600.25214937519799
1.98-2.010.26992570.22574881513899
2.01-2.040.25612590.21174917517699
2.04-2.070.27642610.21274968522999
2.07-2.10.26082590.20624911517099
2.1-2.130.24152600.20454950521099
2.13-2.160.23722590.18544908516799
2.16-2.20.2342610.174849615222100
2.2-2.240.22362600.16534952521299
2.24-2.280.21232600.16924928518899
2.28-2.330.22922600.173449505210100
2.33-2.380.21382600.16764925518599
2.38-2.440.22572620.169649775239100
2.44-2.50.21272610.16684971523299
2.5-2.570.22942620.16164970523299
2.57-2.640.21782600.15614944520499
2.64-2.730.20162600.15524947520799
2.73-2.820.1942590.15844908516798
2.82-2.940.21092590.15764926518599
2.94-3.070.21072600.15954949520999
3.07-3.230.18292610.15914953521499
3.23-3.430.20182620.1664974523699
3.43-3.70.19012610.16234965522699
3.7-4.070.18132610.15494956521798
4.07-4.660.15932600.1454939519997
4.66-5.870.17972600.16254947520797
5.87-49.630.19392700.16455103537396

+
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://pdbjlvh1.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