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- PDB-3tak: Crystal structure of the complex of DHDPS from Acinetobacter baum... -

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Basic information

Entry
Database: PDB / ID: 3tak
TitleCrystal structure of the complex of DHDPS from Acinetobacter baumannii with Pyruvate at 1.4 A resolution
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / DHDPS / TIM Barrel / Lysine biosynthesis / Pyruvate
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / 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: 1.42 Å
AuthorsSingh, A. / Kaushik, S. / Sinha, M. / Tewari, R. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the complex of DHDPS from Acinetobacter baumannii with Pyruvate at 1.4 A resolution
Authors: Singh, A. / Kaushik, S. / Sinha, M. / Tewari, R. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
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 / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,30210
Polymers62,5602
Non-polymers7438
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-5 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.250, 122.420, 52.310
Angle α, β, γ (deg.)90.00, 116.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrodipicolinate synthase / DHDPS


Mass: 31279.842 Da / Num. of mol.: 2 / Fragment: UNP residues 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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M MgCl2, PEG 3350, pH 8, 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: Jul 16, 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: 1.4→61 Å / Num. all: 108756 / Num. obs: 108756 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.068 / Net I/σ(I): 10.8
Reflection shellResolution: 1.42→1.5 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.569 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RK8

3rk8


Resolution: 1.42→25.11 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18774 5424 5 %RANDOM
Rwork0.16361 ---
obs0.16479 103275 99.9 %-
all-103275 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.119 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-0.31 Å2
2---0.55 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.42→25.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 47 654 5091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224509
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.9866118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6185580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95225.93172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21615780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4171518
X-RAY DIFFRACTIONr_chiral_restr0.1520.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213284
X-RAY DIFFRACTIONr_mcbond_it1.2831.52894
X-RAY DIFFRACTIONr_mcangle_it2.13924672
X-RAY DIFFRACTIONr_scbond_it3.55731615
X-RAY DIFFRACTIONr_scangle_it5.7614.51446
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 403 -
Rwork0.296 7600 -
obs--99.58 %

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