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- PDB-4dxv: Crystal structure of Dihydrodipicolinate synthase from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 4dxv
TitleCrystal structure of Dihydrodipicolinate synthase from Acinetobacter baumannii complexed with Mg and Cl ions at 1.80 A resolution
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / DHDPS / TIM Barrel / Lysine biosynthesis / Chloride
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
4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, M. / Kaushik, S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of Dihydrodipicolinate synthase from Acinetobacter baumannii complexed with Mg and Cl ions at 1.80 A resolution
Authors: Kumar, M. / Kaushik, S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)62,7476
Polymers62,5602
Non-polymers1874
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-15 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.350, 122.470, 52.330
Angle α, β, γ (deg.)90.00, 115.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrodipicolinate synthase


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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2M MgCl2, PEG 3350, pH 6.2, 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: Oct 30, 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→61.24 Å / Num. all: 50787 / Num. obs: 50787 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.103 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.56 / % possible all: 98

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Processing

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

3rk8


Resolution: 1.8→61.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.405 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19875 2720 5.1 %RANDOM
Rwork0.15217 ---
all0.15454 50787 --
obs0.15454 50787 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.073 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å20.08 Å2
2---0.64 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→61.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 9 637 5036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224463
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.9796075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09725.93172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6715780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5551518
X-RAY DIFFRACTIONr_chiral_restr0.1640.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213276
X-RAY DIFFRACTIONr_mcbond_it1.251.52894
X-RAY DIFFRACTIONr_mcangle_it2.04824672
X-RAY DIFFRACTIONr_scbond_it3.80131569
X-RAY DIFFRACTIONr_scangle_it6.0544.51403
LS refinement shellResolution: 1.8→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 211 -
Rwork0.225 3689 -
obs--98 %

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