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- PDB-7mjf: Crystal structure of Candidatus Liberibacter solanacearum dihydro... -

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Basic information

Entry
Database: PDB / ID: 7mjf
TitleCrystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / dihydrodipicolinate / Liberibacter
Function / homology
Function and homology information


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
(4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid / (4S)-4-hydroxy-2-oxoheptanedioic acid / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCandidatus Liberibacter solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGilkes, J. / Frampton, R.A. / Board, A.J. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J.
CitationJournal: To Be Published
Title: Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site
Authors: Gilkes, J. / Frampton, R.A. / Board, A.J. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J.
History
DepositionApr 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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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)193,48518
Polymers191,2036
Non-polymers2,28212
Water16,159897
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4956
Polymers63,7342
Non-polymers7614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-14 kcal/mol
Surface area21510 Å2
MethodPISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4956
Polymers63,7342
Non-polymers7614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-14 kcal/mol
Surface area21360 Å2
MethodPISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4956
Polymers63,7342
Non-polymers7614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-14 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.101, 132.881, 155.062
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31867.117 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Liberibacter solanacearum (bacteria)
Gene: dapA, DJ66_0589 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A0F4VK59, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical
ChemComp-E8U / (4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid / HTPA synthase


Mass: 190.151 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C7H10O6 / Details: Succinic acid in 2 stereochemistry conformations / References: 4-hydroxy-tetrahydrodipicolinate synthase
#3: Chemical
ChemComp-ZGM / (4S)-4-hydroxy-2-oxoheptanedioic acid / HTPA synthase


Mass: 190.151 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C7H10O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 897 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG3000, 0.1 M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953723 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953723 Å / Relative weight: 1
ReflectionResolution: 1.925→45.812 Å / Num. obs: 195500 / % possible obs: 99.5 % / Redundancy: 3.9 % / Net I/σ(I): 8.32
Reflection shellResolution: 1.93→1.99 Å

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7LOY

7loy


Resolution: 2.2→45.1 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 9815 5.02 %RANDOM
Rwork0.156 ---
obs0.158 195500 96.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13404 0 144 897 14445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713746
X-RAY DIFFRACTIONf_angle_d0.91618654
X-RAY DIFFRACTIONf_dihedral_angle_d4.0739299
X-RAY DIFFRACTIONf_chiral_restr0.0532164
X-RAY DIFFRACTIONf_plane_restr0.0052437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.33083470.26236105X-RAY DIFFRACTION98
2.225-2.25120.2913160.24496353X-RAY DIFFRACTION97
2.2512-2.27870.29253190.23026067X-RAY DIFFRACTION96
2.2787-2.30750.29263330.21746233X-RAY DIFFRACTION97
2.3075-2.33790.27653460.21096279X-RAY DIFFRACTION99
2.3379-2.36990.26353540.20686311X-RAY DIFFRACTION98
2.3699-2.40370.27372940.20176150X-RAY DIFFRACTION97
2.4037-2.43960.26313870.1976214X-RAY DIFFRACTION98
2.4396-2.47770.23343130.18456374X-RAY DIFFRACTION99
2.4777-2.51840.24083820.1836338X-RAY DIFFRACTION99
2.5184-2.56180.22833460.17936180X-RAY DIFFRACTION99
2.5618-2.60840.27532840.17466491X-RAY DIFFRACTION99
2.6084-2.65850.24153120.17676328X-RAY DIFFRACTION99
2.6585-2.71280.2343400.17516307X-RAY DIFFRACTION99
2.7128-2.77180.28913230.18596335X-RAY DIFFRACTION99
2.7718-2.83620.28063480.1876196X-RAY DIFFRACTION98
2.8362-2.90710.21223440.16236280X-RAY DIFFRACTION98
2.9071-2.98570.26893330.17676308X-RAY DIFFRACTION98
2.9857-3.07360.22713130.17686161X-RAY DIFFRACTION97
3.0736-3.17270.25263520.18676111X-RAY DIFFRACTION96
3.1727-3.28610.22163250.185960X-RAY DIFFRACTION94
3.2861-3.41760.20452930.15966107X-RAY DIFFRACTION95
3.4176-3.57310.18642930.15886004X-RAY DIFFRACTION93
3.5731-3.76140.19673300.14796055X-RAY DIFFRACTION95
3.7614-3.99690.17763230.13116098X-RAY DIFFRACTION95
3.9969-4.30530.14673110.11195982X-RAY DIFFRACTION94
4.3053-4.73820.15653370.10676077X-RAY DIFFRACTION95
4.7382-5.42280.17393230.12016000X-RAY DIFFRACTION94
5.4228-6.82830.17853180.14156060X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 17.4676 Å / Origin y: -2.3157 Å / Origin z: 42.7004 Å
111213212223313233
T0.2544 Å20.02 Å2-0.0487 Å2-0.2663 Å20.0106 Å2--0.3151 Å2
L0.1982 °2-0.0206 °20.2058 °2-0.0843 °2-0.073 °2--0.8215 °2
S-0.0344 Å °0.1057 Å °0.0436 Å °-0.0642 Å °-0.029 Å °0.0749 Å °-0.0818 Å °-0.0287 Å °0.0575 Å °
Refinement TLS groupSelection details: ALL

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