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- PDB-3qze: Crystal Structure of DapA (PA1010) at 1.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 3qze
TitleCrystal Structure of DapA (PA1010) at 1.6 A resolution
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / Alpha beta barrel / Dihydrodipicolinate synthase / cytoplasmic
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / L-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
4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsSchnell, R. / Sandalova, T. / Schneider, G.
CitationJournal: Plos One / Year: 2012
Title: Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.
Authors: Schnell, R. / Oehlmann, W. / Sandalova, T. / Braun, Y. / Huck, C. / Maringer, M. / Singh, M. / Schneider, G.
History
DepositionMar 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Structure summary
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,3188
Polymers136,1764
Non-polymers1424
Water15,763875
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1594
Polymers68,0882
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-40 kcal/mol
Surface area20550 Å2
MethodPISA
2
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1594
Polymers68,0882
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-39 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.110, 51.740, 140.350
Angle α, β, γ (deg.)95.70, 90.02, 113.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dihydrodipicolinate synthase / DHDPS


Mass: 34044.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-tag and TEV protease site / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dapA, dapA (PA1010), PA1010 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I4W3, dihydrodipicolinate synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M Tris-HCl pH 7.6, 0.2 M MgCl2, 18% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2010
Details: channel cut ESRF monochromator and a new torodial focusing mirror
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.59→41.25 Å / Num. all: 139082 / Num. obs: 139082 / % possible obs: 92.7 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 2 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 9.5
Reflection shellResolution: 1.59→1.67 Å / Redundancy: 2 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.1 / Num. unique all: 20245 / Rsym value: 0.281 / % possible all: 92.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OJP chain-A edited

2ojp


Resolution: 1.59→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.385 / SU ML: 0.054 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(I): 3.1 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 7011 5 %RANDOM
Rwork0.14683 ---
all0.14948 132070 --
obs0.14948 132070 92.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.14 Å2
2--0.53 Å20.37 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.59→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 4 875 9647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229020
X-RAY DIFFRACTIONr_bond_other_d0.0010.026089
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.97112277
X-RAY DIFFRACTIONr_angle_other_deg1.13314906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97951185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15723.622370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.447151540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5791578
X-RAY DIFFRACTIONr_chiral_restr0.1330.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021715
X-RAY DIFFRACTIONr_mcbond_it1.9311.55815
X-RAY DIFFRACTIONr_mcbond_other0.9241.52360
X-RAY DIFFRACTIONr_mcangle_it2.68529379
X-RAY DIFFRACTIONr_scbond_it4.04133205
X-RAY DIFFRACTIONr_scangle_it5.8034.52884
X-RAY DIFFRACTIONr_rigid_bond_restr2.119315109
X-RAY DIFFRACTIONr_sphericity_free9.6763879
X-RAY DIFFRACTIONr_sphericity_bonded3.517314943
LS refinement shellResolution: 1.586→1.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 487 -
Rwork0.199 9583 -
obs--91 %

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