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- PDB-3dz1: Crystal structure of Dihydrodipicolinate Synthase from Rhodopseud... -

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Basic information

Entry
Database: PDB / ID: 3dz1
TitleCrystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 1.87A resolution
ComponentsDihydrodipicolinate synthase
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


4-hydroxy-tetrahydrodipicolinate synthase activity / cytosol
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
Dihydrodipicolinate synthase family protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 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 1.87A resolution
Authors: Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)34,7551
Polymers34,7551
Non-polymers00
Water5,945330
1
A: Dihydrodipicolinate synthase

A: Dihydrodipicolinate synthase

A: Dihydrodipicolinate synthase

A: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)139,0214
Polymers139,0214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area10560 Å2
ΔGint-26 kcal/mol
Surface area41500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.463, 84.264, 114.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Dihydrodipicolinate synthase


Mass: 34755.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Top10-Invitrogen
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: palustris / Gene: RPA3190 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: Q6N4Z3, dihydrodipicolinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25%PEG 1,500 0.1M Bis-Tris pH 6.5 1.4% Butanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 28, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 26518 / Num. obs: 26518 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.1
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 12.6 / Num. unique all: 2577 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.87→33.85 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1016 -RANDOM
Rwork0.19 ---
all0.21 26250 --
obs0.21 26250 98.6 %-
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.87→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 0 330 2625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTION(A)0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shellResolution: 1.87→1.99 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.218 163 -
Rwork0.194 --
obs-3955 98.6 %

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