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- PDB-3rk8: Crystal structure of the chloride inhibited dihydrodipicolinate s... -

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Basic information

Entry
Database: PDB / ID: 3rk8
TitleCrystal structure of the chloride inhibited dihydrodipicolinate synthase from Acinetobacter baumannii complexed with pyruvate at 1.8 A resolution
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / DHDPS / TIM Barrel / Lysine biosynthesis / Chloride / Pyruvate
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 / metal ion binding / 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
DI(HYDROXYETHYL)ETHER / PYRUVIC ACID / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKaushik, S. / Singh, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the chloride inhibited dihydrodipicolinate synthase from Acinetobacter baumannii complexed with pyruvate at 1.8 A resolution
Authors: Kaushik, S. / Singh, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,84817
Polymers62,5602
Non-polymers1,28815
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-14 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.251, 122.266, 52.564
Angle α, β, γ (deg.)90.00, 116.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydrodipicolinate synthase /


Mass: 31279.842 Da / Num. of mol.: 2 / Fragment: DHDPS, residues in UNP 7-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 19606 / Gene: dhdps, HMPREF0010_03414 / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: D0CFC3, dihydrodipicolinate synthase

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Non-polymers , 5 types, 618 molecules

#2: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M MgCl2, PEG 3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2011 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 53625 / Num. obs: 53625 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.091 / Net I/σ(I): 23.1
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.539 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PUD

3pud


Resolution: 1.8→47.12 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18824 2721 5.1 %RANDOM
Rwork0.14809 ---
obs0.15016 50757 99.73 %-
all-53625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.198 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å2-0.08 Å2
2---0.97 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 82 603 5075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_mcbond_it1.2971.52894
X-RAY DIFFRACTIONr_mcangle_it2.10124672
X-RAY DIFFRACTIONr_scbond_it3.94531631
X-RAY DIFFRACTIONr_scangle_it6.4894.51465
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 183 -
Rwork0.223 3636 -
obs--97.2 %

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