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- PDB-1xky: Crystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935)... -

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Basic information

Entry
Database: PDB / ID: 1xky
TitleCrystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935) from Bacillus Anthracis at 1.94A Resolution.
Componentsdihydrodipicolinate synthase
KeywordsLYASE / dihydrodipicolinate synthase / TIM barrel / crystal structure / lysine biosynthesis / SPINE
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
: / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLevdikov, V. / Blagova, E. / Fogg, M.J. / Brannigan, J.A. / Milioti, N. / Wilkinson, A.J. / Wilson, K.S.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 A resolution
Authors: Blagova, E. / Levdikov, V. / Milioti, N. / Fogg, M.J. / Kalliomaa, A.K. / Brannigan, J.A. / Wilson, K.S. / Wilkinson, A.J.
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)129,67514
Polymers129,2844
Non-polymers39110
Water31,4901748
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-73 kcal/mol
Surface area40560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.203, 126.882, 173.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
dihydrodipicolinate synthase


Mass: 32321.049 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: DapA-2 / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q81WN7, UniProt: A0A6L7H340*PLUS, dihydrodipicolinate synthase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1748 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 5000 MME, KSCN, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54189 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 2004 / Details: multilayer optics
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54189 Å / Relative weight: 1
ReflectionResolution: 1.94→20 Å / Num. all: 87118 / Num. obs: 87118 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.2
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3 / Num. unique all: 7624 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DHP

1dhp


Resolution: 1.94→19.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.041 / SU ML: 0.089 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.154 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19719 4360 5 %RANDOM
Rwork0.1534 ---
all0.15555 87004 --
obs0.15555 82644 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.158 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8758 0 10 1748 10516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228910
X-RAY DIFFRACTIONr_bond_other_d0.0010.028453
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.97712132
X-RAY DIFFRACTIONr_angle_other_deg0.898319691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64251168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61425.466322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.939151545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3951533
X-RAY DIFFRACTIONr_chiral_restr0.0950.21508
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021550
X-RAY DIFFRACTIONr_nbd_refined0.2290.22006
X-RAY DIFFRACTIONr_nbd_other0.1640.28542
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24519
X-RAY DIFFRACTIONr_nbtor_other0.0790.24921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.21410
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.231
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.273
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4331.55818
X-RAY DIFFRACTIONr_mcbond_other0.0871.52370
X-RAY DIFFRACTIONr_mcangle_it0.83929500
X-RAY DIFFRACTIONr_scbond_it1.53233120
X-RAY DIFFRACTIONr_scangle_it2.674.52630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 281 -
Rwork0.209 5332 -
obs-5332 100 %

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