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- PDB-7klq: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59A mutant w... -

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Basic information

Entry
Database: PDB / ID: 7klq
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59A mutant with pyruvate bound in the active 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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: H59 PLAYS THE MOST VITAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS ENZYME
Authors: Saran, S. / Skovpen, Y. / Majdi Yazdi, M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionOct 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)206,65830
Polymers204,7096
Non-polymers1,94924
Water13,709761
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23113
Polymers68,2362
Non-polymers99411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-30 kcal/mol
Surface area22180 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,93711
Polymers68,2362
Non-polymers7009
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint1 kcal/mol
Surface area22620 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4916
Polymers68,2362
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-22 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.974, 231.827, 202.228
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-514-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 24 or (resid 25...
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
11LYSLYSGLUGLU(chain A and (resid 3 through 24 or (resid 25...AA3 - 2415 - 36
12GLNGLNGLNGLN(chain A and (resid 3 through 24 or (resid 25...AA2537
13LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...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
23LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
27LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 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
46LYSLYSPHEPHE(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
63LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 29815 - 310
64LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 29815 - 310
65LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 29815 - 310
66LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 29815 - 310
67LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 29815 - 310

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 34118.191 Da / Num. of mol.: 6
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

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Non-polymers , 6 types, 785 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.9 M Magnesium acetate, 8 % PEG8000, 0.1 M Sodium acetate (pH 7.4),

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→22.76 Å / Num. obs: 69244 / % possible obs: 99.82 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 32.6
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.01 / Num. unique obs: 6842 / % possible all: 100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.5→22.76 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 3482 5.05 %
Rwork0.2053 65475 -
obs0.2075 68957 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.98 Å2 / Biso mean: 15.128 Å2 / Biso min: 2.4 Å2
Refinement stepCycle: final / Resolution: 2.5→22.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13584 0 126 761 14471
Biso mean--19.42 15.15 -
Num. residues----1776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5358X-RAY DIFFRACTION4.426TORSIONAL
12B5358X-RAY DIFFRACTION4.426TORSIONAL
13C5358X-RAY DIFFRACTION4.426TORSIONAL
14D5358X-RAY DIFFRACTION4.426TORSIONAL
15E5358X-RAY DIFFRACTION4.426TORSIONAL
16F5358X-RAY DIFFRACTION4.426TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.530.30571400.23822576100
2.53-2.570.3141280.23172645100
2.57-2.610.2831310.23232587100
2.61-2.650.29381420.22972602100
2.65-2.690.32041530.22692582100
2.69-2.740.26181250.22792630100
2.74-2.790.27291270.23112587100
2.79-2.840.29781370.23132607100
2.84-2.90.27791580.24272573100
2.9-2.960.28581590.22662595100
2.96-3.030.28561390.22382610100
3.03-3.110.27691620.2162254499
3.11-3.190.32671260.20872637100
3.19-3.290.24281230.2255262299
3.29-3.390.29781460.2152259499
3.39-3.510.29521450.2049257099
3.51-3.650.23211370.2051260299
3.65-3.820.20611360.1909259699
3.82-4.020.19961390.1793262099
4.02-4.270.18651440.17442623100
4.27-4.590.17981180.1729265099
4.59-5.050.21691450.17512651100
5.05-5.770.21331410.19052669100
5.77-7.230.21791390.1962714100
7.23-100.17481420.16462789100

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