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- PDB-7m06: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7m06
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant with R,R-bislysine bound at the allosteric site at 2.7 Angstrom
Components4-hydroxy-tetrahydrodipicolinate synthaseDihydrodipicolinate synthase
KeywordsLYASE
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm
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
Chem-3VN / 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: 2.7 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: B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS
Authors: Saran, S. / Sanders, D.A.R.
History
DepositionMar 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,13122
Polymers136,4014
Non-polymers1,73118
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-97 kcal/mol
Surface area40160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.030, 84.290, 200.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 70 or resid 72...
21(chain B and (resid 3 through 70 or resid 72...
31(chain C and (resid 3 through 70 or resid 72 through 298))
41(chain D and (resid 3 through 70 or resid 72...

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
11LYSLYSCYSCYS(chain A and (resid 3 through 70 or resid 72...AA3 - 7015 - 82
12GLYGLYTHRTHR(chain A and (resid 3 through 70 or resid 72...AA72 - 7384 - 85
13LYSLYSLYSLYS(chain A and (resid 3 through 70 or resid 72...AA7486
14LYSLYSPHEPHE(chain A and (resid 3 through 70 or resid 72...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 70 or resid 72...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 70 or resid 72...AA3 - 29815 - 310
17LYSLYSPHEPHE(chain A and (resid 3 through 70 or resid 72...AA3 - 29815 - 310
21LYSLYSCYSCYS(chain B and (resid 3 through 70 or resid 72...BB3 - 7015 - 82
22GLYGLYTHRTHR(chain B and (resid 3 through 70 or resid 72...BB72 - 7384 - 85
23LYSLYSLYSLYS(chain B and (resid 3 through 70 or resid 72...BB7486
24LYSLYSPHEPHE(chain B and (resid 3 through 70 or resid 72...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 70 or resid 72...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 70 or resid 72...BB3 - 29815 - 310
27LYSLYSPHEPHE(chain B and (resid 3 through 70 or resid 72...BB3 - 29815 - 310
31LYSLYSCYSCYS(chain C and (resid 3 through 70 or resid 72 through 298))CC3 - 7015 - 82
32GLYGLYPHEPHE(chain C and (resid 3 through 70 or resid 72 through 298))CC72 - 29884 - 310
41LYSLYSCYSCYS(chain D and (resid 3 through 70 or resid 72...DD3 - 7015 - 82
42GLYGLYTHRTHR(chain D and (resid 3 through 70 or resid 72...DD72 - 7384 - 85
43LYSLYSLYSLYS(chain D and (resid 3 through 70 or resid 72...DD7486
44ASPASPPHEPHE(chain D and (resid 3 through 70 or resid 72...DD2 - 29814 - 310
45ASPASPPHEPHE(chain D and (resid 3 through 70 or resid 72...DD2 - 29814 - 310
46ASPASPPHEPHE(chain D and (resid 3 through 70 or resid 72...DD2 - 29814 - 310
47ASPASPPHEPHE(chain D and (resid 3 through 70 or resid 72...DD2 - 29814 - 310

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 34100.219 Da / Num. of mol.: 4 / Mutation: Y110F
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, 110 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3VN / (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid / bis-Lysine


Mass: 318.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 288.15 K / Method: microbatch / Details: 0.2 M Magnesium acetate, 10% PEG 8000 / PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 24, 2021
RadiationMonochromator: Double beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→43.15 Å / Num. obs: 34342 / % possible obs: 99.73 % / Redundancy: 14 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0351 / Rrim(I) all: 0.04964 / Net I/σ(I): 17.29
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 0.2826 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 3362 / CC1/2: 0.859 / CC star: 0.961 / Rrim(I) all: 0.3997 / % possible all: 99.82

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Processing

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

4ly8


Resolution: 2.7→43.15 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1717 5 %
Rwork0.1936 32615 -
obs0.1961 34332 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.22 Å2 / Biso mean: 47.6138 Å2 / Biso min: 19.36 Å2
Refinement stepCycle: final / Resolution: 2.7→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9056 0 108 92 9256
Biso mean--77.85 40.65 -
Num. residues----1185
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3544X-RAY DIFFRACTION3.283TORSIONAL
12B3544X-RAY DIFFRACTION3.283TORSIONAL
13C3544X-RAY DIFFRACTION3.283TORSIONAL
14D3544X-RAY DIFFRACTION3.283TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.780.33511420.29332678100
2.78-2.870.30191400.24612662100
2.87-2.970.31021400.23252674100
2.97-3.090.28391420.23972699100
3.09-3.230.31941400.22982663100
3.23-3.40.2721420.21592708100
3.4-3.610.25951420.20132688100
3.61-3.890.22941430.18342719100
3.89-4.280.23571430.16762725100
4.29-4.90.19911440.15882722100
4.9-6.180.21761460.18392773100
6.18-100.19231530.1743290499
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)
12.65490.42090.0012.0975-1.1034.2431-0.02360.04230.69530.11340.0712-0.028-0.5186-0.0301-0.18160.49280.06720.10370.34360.02980.5201-75.488132.28384.863
23.0661-0.3546-0.5131-0.1708-0.24731.26440.03580.24170.60590.28520.0545-0.0292-0.2027-0.0166-0.05940.4635-0.06630.02410.30920.00550.4531-63.191929.690389.8111
34.91411.2139-0.97891.9732-1.38434.9840.1032-0.45180.2310.1568-0.05530.0793-0.4110.2813-0.07090.34070.00890.01110.2919-0.01210.3311-57.517419.337693.4064
42.2979-0.2677-0.53334.4588-2.56991.5210.15090.0433-0.0609-0.1586-0.11920.00690.2514-0.0391-0.14110.4140.0243-0.01570.37160.02450.3297-65.701612.656195.7744
52.6810.5916-1.1691.969-0.93471.73870.09280.41760.1113-0.03790.04430.2579-0.0998-0.2099-0.1540.27710.04-0.00170.32620.00680.3503-81.44817.113180.7513
60.366-0.56250.19980.7691.16254.95090.08820.05080.13590.1150.18620.0004-0.34090.2717-0.35650.4309-0.06350.01330.38160.04620.4317-39.505427.621970.3953
74.6063-2.1661-1.85323.18870.90014.7855-0.17920.06320.31450.1227-0.0053-0.12870.0170.53790.10370.3533-0.12490.04870.30760.01860.3323-36.282627.970671.3023
81.8796-0.79081.62791.3702-0.83612.7106-0.1476-0.22530.4269-0.12170.25270.1958-0.58170.0393-0.13450.441-0.0363-0.00430.31230.04380.4215-45.867134.571766.9176
93.0571-1.0801-0.50250.81040.8221.2471-0.0870.02380.3165-0.1924-0.00950.1364-0.1287-0.36770.15820.44380.05290.0550.28740.01480.2995-55.23326.11867.842
109.26440.9543-0.73543.6123-0.20453.77430.15160.76660.4075-0.2503-0.05260.2286-0.4269-0.2018-0.08990.36840.01110.01110.40490.07020.3193-58.153926.472360.1869
111.3763-0.05950.92662.6975-0.48822.2892-0.12930.1930.0487-0.17250.02630.0362-0.2688-0.71510.05930.3468-0.01390.04450.37990.06370.3236-58.523817.255960.9779
122.42871.77780.02785.17973.36032.9881-0.131-0.096-0.04690.10090.0174-0.00370.1408-0.27050.14170.302-0.024-0.00250.4210.03790.3574-52.697514.278257.6643
136.2672-2.9183.65775.8138-1.88972.4191-0.06880.08740.10290.4669-0.2532-0.0412-0.17660.06520.20210.402-0.01730.09120.40580.04330.3391-45.291612.000158.3516
140.9943-0.6142-1.26641.78540.02112.586-0.0101-0.09540.06190.01460.0193-0.18270.21880.22450.03310.2857-0.0086-0.01440.31370.00470.3852-35.543812.199767.6662
152.7814-2.1169-1.80761.86760.58643.77120.2755-1.03690.51690.067-0.118-0.2133-0.13520.8007-0.14380.42290.0094-0.04150.5558-0.02260.3155-38.045123.161785.2786
162.88360.9292-0.41164.6048-0.6610.62890.1746-0.557-0.19230.4534-0.1989-0.60490.15320.50790.11150.55750.0934-0.13570.493-0.0030.4764-29.758111.514580.8579
178.23792.41120.76981.53260.30283.087-0.03390.1865-0.6285-0.03190.00110.15040.223-0.15550.16030.41720.01990.04110.3233-0.02530.3819-55.8767-21.233455.4944
184.42440.3221-3.32712.7322-1.27634.014-0.06730.6056-0.5883-0.1077-0.12150.11920.0755-0.37750.01440.3861-0.08060.01550.3835-0.12640.3792-56.981-21.636652.3948
190.7601-0.66720.06851.25420.9254.25770.01840.0596-0.41850.1315-0.01320.06340.4184-0.1003-0.14540.34050.00180.04510.2935-0.00160.4248-52.0589-25.7164.3548
200.9940.6313-0.59930.00510.0122.1460.0524-0.0229-0.0593-0.1081-0.0507-0.09610.00620.1623-0.03480.36990.02190.02570.3333-0.00030.3637-44.7539-10.709564.9265
215.96362.7239-3.9162.8378-2.37283.2728-0.19480.2984-0.0508-0.11080.10570.03060.0562-0.18830.20450.33870.0311-0.01170.3468-0.00380.2683-61.1701-8.124152.7234
228.60540.6192-2.72692.5988-1.01167.7036-0.32060.83310.3719-0.45680.18310.24770.2898-0.55670.03510.55790.0206-0.09420.5129-0.01650.4238-66.9537-5.331846.445
232.7065-2.24680.50731.7144-0.04031.1739-0.22620.1229-0.61930.29650.18390.2668-0.05240.2146-0.11490.36550.01480.0260.39650.04760.3192-67.6358-23.113791.6394
247.11550.6663-2.0934.0590.86384.995-0.01970.0211-0.72270.03490.1354-0.11750.4610.0195-0.0460.40930.01670.05770.29170.08020.4861-67.4866-26.742592.5847
250.95720.28350.70960.90090.45810.6772-0.22090.187-0.7195-0.19110.10550.05540.6269-0.28670.19220.4391-0.01740.04430.32310.01230.4826-75-26.021782.4715
262.55281.9595-1.01284.2957-1.23586.0405-0.1972-0.40440.228-0.2058-0.05880.28840.3464-0.0160.27790.35590.08970.01980.4491-0.01950.337-70.9114-18.422776.752
274.4588-1.8549-0.69070.836-0.39734.414-0.00650.3083-0.3186-0.0646-0.11450.12190.0318-0.56030.03120.3036-0.0380.02780.3278-0.01280.3483-77.6351-12.978874.956
282.2974-3.8933-0.08815.56320.05954.9843-0.15410.08960.28570.29520.1905-0.13870.19970.1610.2020.290.00540.02370.34620.0390.2794-78.7275-5.789882.0614
291.9469-1.60371.16811.95720.79773.58480.25270.26860.28210.1903-0.2517-0.30640.3378-0.0933-0.11090.3828-0.06460.08930.37420.07990.4415-77.1515-4.938889.7464
305.6677-3.4977-0.94625.3039-0.18070.5399-0.108-0.1614-0.62440.03640.20110.44150.28020.1666-0.1490.4893-0.0529-0.01570.3993-0.01390.2991-72.9742-10.267298.6427
316.3388-1.3209-2.26932.18210.41732.00740.3571-0.01470.3250.0123-0.0646-0.3055-0.3808-0.0911-0.22240.47720.0162-0.06750.2576-0.02230.3322-69.1292-2.7631100.4377
322.1558-0.5611-1.63341.16782.26734.5284-0.1792-0.216-0.1594-0.0135-0.10610.15140.1120.37960.3860.36130.0910.00350.40550.06560.389-53.5769-18.611793.2946
331.5255-1.0714-1.39180.73980.96261.40430.22110.0653-0.04350.3393-0.0923-0.1061-0.7061-0.0155-0.09280.5528-0.0259-0.12580.4274-0.03080.3415-54.148-10.6786102.9434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 69 )A3 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 115 )A70 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 158 )A116 - 158
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 191 )A159 - 191
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 298 )A192 - 298
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 23 )B3 - 23
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 55 )B24 - 55
8X-RAY DIFFRACTION8chain 'B' and (resid 56 through 98 )B56 - 98
9X-RAY DIFFRACTION9chain 'B' and (resid 99 through 115 )B99 - 115
10X-RAY DIFFRACTION10chain 'B' and (resid 116 through 138 )B116 - 138
11X-RAY DIFFRACTION11chain 'B' and (resid 139 through 158 )B139 - 158
12X-RAY DIFFRACTION12chain 'B' and (resid 159 through 181 )B159 - 181
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 200 )B182 - 200
14X-RAY DIFFRACTION14chain 'B' and (resid 201 through 262 )B201 - 262
15X-RAY DIFFRACTION15chain 'B' and (resid 263 through 279 )B263 - 279
16X-RAY DIFFRACTION16chain 'B' and (resid 280 through 298 )B280 - 298
17X-RAY DIFFRACTION17chain 'C' and (resid 3 through 23 )C3 - 23
18X-RAY DIFFRACTION18chain 'C' and (resid 24 through 55 )C24 - 55
19X-RAY DIFFRACTION19chain 'C' and (resid 56 through 115 )C56 - 115
20X-RAY DIFFRACTION20chain 'C' and (resid 116 through 226 )C116 - 226
21X-RAY DIFFRACTION21chain 'C' and (resid 227 through 279 )C227 - 279
22X-RAY DIFFRACTION22chain 'C' and (resid 280 through 298 )C280 - 298
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 23 )D3 - 23
24X-RAY DIFFRACTION24chain 'D' and (resid 24 through 70 )D24 - 70
25X-RAY DIFFRACTION25chain 'D' and (resid 71 through 98 )D71 - 98
26X-RAY DIFFRACTION26chain 'D' and (resid 99 through 115 )D99 - 115
27X-RAY DIFFRACTION27chain 'D' and (resid 116 through 158 )D116 - 158
28X-RAY DIFFRACTION28chain 'D' and (resid 159 through 181 )D159 - 181
29X-RAY DIFFRACTION29chain 'D' and (resid 182 through 200 )D182 - 200
30X-RAY DIFFRACTION30chain 'D' and (resid 201 through 226 )D201 - 226
31X-RAY DIFFRACTION31chain 'D' and (resid 227 through 248 )D227 - 248
32X-RAY DIFFRACTION32chain 'D' and (resid 249 through 279 )D249 - 279
33X-RAY DIFFRACTION33chain 'D' and (resid 280 through 298 )D280 - 298

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