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- PDB-3eb2: Crystal structure of Dihydrodipicolinate Synthase from Rhodopseud... -

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Basic information

Entry
Database: PDB / ID: 3eb2
TitleCrystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 2.0A resolution
ComponentsPutative dihydrodipicolinate synthetase
KeywordsLYASE / LYSINE BIOSYNTHESIS / PYRUVATE / TIM BARREL / NYSGXRC / 11102O / PSI2. / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


dihydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity
Similarity search - Function
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
TRIETHYLENE GLYCOL / Dihydrodipicolinate synthetase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsSatyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 2.0A resolution
Authors: Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative dihydrodipicolinate synthetase
B: Putative dihydrodipicolinate synthetase
C: Putative dihydrodipicolinate synthetase
D: Putative dihydrodipicolinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3346
Polymers130,0334
Non-polymers3002
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-42 kcal/mol
Surface area40860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.746, 120.852, 135.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative dihydrodipicolinate synthetase


Mass: 32508.338 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Top10-Invitrogen
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: palustris / Gene: dapA1, RPA1571 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon+RIL / References: UniProt: Q6N9H8, dihydrodipicolinate synthase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 1,500, 0.1M Bis-Tris pH 5.5, 0.025M Trimethylamine hydrochloride., VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 10, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 82938 / Num. obs: 82938 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.8
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 11.1 / Num. unique all: 7055 / % possible all: 84.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.04→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3207 -RANDOM
Rwork0.212 ---
all0.212 79800 --
obs-79800 95.4 %-
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å20 Å20 Å2
2--0.69 Å20 Å2
3----4.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8774 0 20 605 9399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angles_deg21.2
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.289 530 -
Rwork0.239 --
obs-7055 90.7 %

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