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- PDB-4mlr: dihydrodipicolinate synthase from C. jejuni, Y110F mutation with ... -

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Basic information

Entry
Database: PDB / ID: 4mlr
Titledihydrodipicolinate synthase from C. jejuni, Y110F mutation with pyruvate and Lysine
Componentsdihydrodipicolinate synthase
KeywordsLYASE / schiff-base / aldolase / TIM barrel
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 class I / Aldolase-type TIM barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / LYSINE / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciescampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsConly, C.J.T.
CitationJournal: Biochemistry / Year: 2014
Title: Tyrosine 110 Plays a Critical Role in Regulating the Allosteric Inhibition of Campylobacter jejuni Dihydrodipicolinate Synthase by Lysine.
Authors: Conly, C.J. / Skovpen, Y.V. / Li, S. / Palmer, D.R. / Sanders, D.A.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Data collection
Revision 1.2Apr 1, 2015Group: Structure summary
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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: dihydrodipicolinate synthase
B: dihydrodipicolinate synthase
C: dihydrodipicolinate synthase
D: dihydrodipicolinate synthase
E: dihydrodipicolinate synthase
F: dihydrodipicolinate synthase
G: dihydrodipicolinate synthase
H: dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,09235
Polymers270,0068
Non-polymers3,08627
Water3,639202
1
A: dihydrodipicolinate synthase
B: dihydrodipicolinate synthase
C: dihydrodipicolinate synthase
D: dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,68018
Polymers135,0034
Non-polymers1,67714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-35 kcal/mol
Surface area39440 Å2
MethodPISA
2
E: dihydrodipicolinate synthase
F: dihydrodipicolinate synthase
G: dihydrodipicolinate synthase
H: dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,41217
Polymers135,0034
Non-polymers1,40913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-42 kcal/mol
Surface area39440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.983, 97.610, 131.398
Angle α, β, γ (deg.)90.00, 92.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 33750.770 Da / Num. of mol.: 8 / Mutation: Y110F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) campylobacter jejuni (Campylobacter) / Gene: dapA / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

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Non-polymers , 7 types, 229 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% PEG4000, 0.2 M sodium acetate, 0.1 mM TRIS, pH 8.5, VAPOUR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 12, 2012
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→43.45 Å / Num. all: 116487 / Num. obs: 116487 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.17 % / Biso Wilson estimate: 43.88 Å2 / Rmerge(I) obs: 0.147 / Χ2: 1.15 / Net I/σ(I): 4.5 / Scaling rejects: 3672
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.284.240.7841.449430116341.31100
2.28-2.374.250.7321.649397115941.26100
2.37-2.484.250.6991.749394116161.26100
2.48-2.614.250.6311.949257115831.24100
2.61-2.774.230.5542.249300116281.23100
2.77-2.994.210.4652.749228116521.23100
2.99-3.294.140.3473.548396116241.2399.9
3.29-3.763.990.1865.747271116531.0399.7
3.76-4.744.080.08611.548529116670.8299.7
4.74-43.454.070.07613.349283118360.8399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.9.7Ldata scaling
d*TREK9.9.9.7Ldata reduction
MOLREPphasing
PHENIXdev_1356refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.2→43.446 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7511 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 31.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 5833 5.01 %random
Rwork0.2145 ---
all0.2172 116434 --
obs0.2172 116434 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.53 Å2 / Biso mean: 50.2732 Å2 / Biso min: 24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18178 0 206 202 18586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318685
X-RAY DIFFRACTIONf_angle_d0.8625193
X-RAY DIFFRACTIONf_chiral_restr0.0572910
X-RAY DIFFRACTIONf_plane_restr0.0033215
X-RAY DIFFRACTIONf_dihedral_angle_d14.017055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.38782020.3337103912100
2.225-2.25120.38311870.354236013788100
2.2512-2.27860.41111960.341937293925100
2.2786-2.30750.41742050.329536453850100
2.3075-2.33780.35721940.313237063900100
2.3378-2.36990.331980.303236443842100
2.3699-2.40370.36551870.29636653852100
2.4037-2.43960.3491780.289837033881100
2.4396-2.47770.37122080.285236733881100
2.4777-2.51830.37081720.278137013873100
2.5183-2.56170.35112070.25936523859100
2.5617-2.60830.33831840.253836653849100
2.6083-2.65850.32642010.253736823883100
2.6585-2.71270.32971890.250636873876100
2.7127-2.77170.34831810.249236853866100
2.7717-2.83620.36472010.265137063907100
2.8362-2.90710.30271830.257536813864100
2.9071-2.98570.31861910.258736873878100
2.9857-3.07350.30091690.25137003869100
3.0735-3.17270.30192200.235336783898100
3.1727-3.2860.29121960.235636563852100
3.286-3.41760.28372310.241736633894100
3.4176-3.5730.31512140.220336643878100
3.573-3.76130.25381800.195436983878100
3.7613-3.99680.25361820.185136933875100
3.9968-4.30520.23261980.168837233921100
4.3052-4.73790.17671750.153136933868100
4.7379-5.42240.20442240.1643694391899
5.4224-6.82740.21931780.193237353913100
6.8274-43.45460.20162020.17233782398499
Refinement TLS params.Method: refined / Origin x: 45.0656 Å / Origin y: -16.0673 Å / Origin z: 95.0766 Å
111213212223313233
T0.3279 Å2-0.009 Å20.0446 Å2-0.2828 Å20.0062 Å2--0.3254 Å2
L0.3176 °2-0.0909 °20.3279 °2-0.1575 °2-0.1043 °2--0.3591 °2
S0.0347 Å °-0.0649 Å °-0.0025 Å °0.041 Å °-0.0168 Å °0.0301 Å °0.0843 Å °-0.037 Å °-0.0165 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 298
2X-RAY DIFFRACTION1allB3 - 298
3X-RAY DIFFRACTION1allC4 - 298
4X-RAY DIFFRACTION1allD3 - 297
5X-RAY DIFFRACTION1allE5 - 298
6X-RAY DIFFRACTION1allF3 - 298
7X-RAY DIFFRACTION1allG3 - 298
8X-RAY DIFFRACTION1allH4 - 298
9X-RAY DIFFRACTION1allA1 - 301
10X-RAY DIFFRACTION1allF1 - 301
11X-RAY DIFFRACTION1allH1 - 301
12X-RAY DIFFRACTION1allE1 - 301
13X-RAY DIFFRACTION1allG1 - 301
14X-RAY DIFFRACTION1allC1 - 301
15X-RAY DIFFRACTION1allA1 - 302
16X-RAY DIFFRACTION1allB1 - 301
17X-RAY DIFFRACTION1allB1 - 302
18X-RAY DIFFRACTION1allC1 - 302
19X-RAY DIFFRACTION1allF1 - 302
20X-RAY DIFFRACTION1allH1 - 302
21X-RAY DIFFRACTION1allB1 - 303
22X-RAY DIFFRACTION1allA1 - 303
23X-RAY DIFFRACTION1allG1 - 302
24X-RAY DIFFRACTION1allD1 - 301
25X-RAY DIFFRACTION1allG1 - 303
26X-RAY DIFFRACTION1allE1 - 302
27X-RAY DIFFRACTION1allB - D1 - 423
28X-RAY DIFFRACTION1allC1 - 303
29X-RAY DIFFRACTION1allF1 - 303
30X-RAY DIFFRACTION1allA1 - 304
31X-RAY DIFFRACTION1allA1 - 305
32X-RAY DIFFRACTION1allG1 - 304
33X-RAY DIFFRACTION1allC1 - 304
34X-RAY DIFFRACTION1allA1 - 306
35X-RAY DIFFRACTION1allE1 - 303
36X-RAY DIFFRACTION1allE1 - 304

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