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- PDB-2ehh: Crystal structure of dihydrodipicolinate synthase from aquifex ae... -

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Basic information

Entry
Database: PDB / ID: 2ehh
TitleCrystal structure of dihydrodipicolinate synthase from aquifex aeolicus
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / dihydrodipicolinate synthase / Aquifex aeolicus / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
PHOSPHATE ION / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of dihydrodipicolinate synthase from aquifex aeolicus
Authors: Kumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S.
History
DepositionMar 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
E: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0296
Polymers130,8394
Non-polymers1902
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-78 kcal/mol
Surface area40580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.321, 146.953, 97.877
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dihydrodipicolinate synthase / DHDPS


Mass: 32709.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: AQ_1143 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL / References: UniProt: O67216, dihydrodipicolinate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 291 K / Method: liquid diffusion / pH: 8
Details: 0.4M NaH2PO4, 1.6M K2HPO4, imidazole, 0.2M NaCl, pH 8.0, LIQUID DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 20, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 126980 / Num. obs: 126980 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.091
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.465 / Num. unique all: 12562 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o5k

1o5k


Resolution: 1.9→19.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 102197.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3739 3 %RANDOM
Rwork0.21 ---
obs0.21 123309 96.6 %-
all-126980 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.5918 Å2 / ksol: 0.424247 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-2.07 Å2
2---0.31 Å20 Å2
3---1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9092 0 10 489 9591
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 526 2.9 %
Rwork0.249 17885 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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