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- PDB-3k3p: Crystal Structure of the Apo Form of D-Alanine:D-Alanine Ligase (... -

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Basic information

Entry
Database: PDB / ID: 3k3p
TitleCrystal Structure of the Apo Form of D-Alanine:D-Alanine Ligase (DDl) from Streptococcus mutans
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / D-alanyl-alanine synthetase / ATP-binding / Cell shape / Cell wall biogenesis/degradation / Magnesium / Manganese / Metal-binding / Nucleotide-binding / Peptidoglycan synthesis
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsLu, Y.
CitationJournal: Protein Pept.Lett. / Year: 2010
Title: Crystal structure of the Apo form of D-Alanine:D-Alanine ligase (DDl) from Streptococcus mutans.
Authors: Lu, Y. / Xu, H. / Zhao, X.
History
DepositionOct 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2019Group: Advisory / Data collection / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)84,8492
Polymers84,8492
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.502, 79.502, 109.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein D-alanine--D-alanine ligase / D-alanylalanine synthetase / D-Ala-D-Ala ligase


Mass: 42424.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: ddl / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95803, D-alanine-D-alanine ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M magnesium sulfate, 0.05M HEPES, 1.2M lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Dec 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.23→68.85 Å / Num. obs: 37656 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 16.3
Reflection shellResolution: 2.23→2.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.2 / Num. unique all: 5526 / Rsym value: 0.605 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrysalisProdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I87

2i87


Resolution: 2.23→17.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1921 5.1 %RANDOM
Rwork0.196 ---
obs0.199 37611 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.52 Å2 / Biso mean: 29.139 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.23→17.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 0 150 5080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225001
X-RAY DIFFRACTIONr_angle_refined_deg1.931.9916766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46125.577208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94315909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7281520
X-RAY DIFFRACTIONr_chiral_restr0.1250.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023648
X-RAY DIFFRACTIONr_nbd_refined0.2150.22232
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.26
X-RAY DIFFRACTIONr_mcbond_it1.171.53156
X-RAY DIFFRACTIONr_mcangle_it2.10525118
X-RAY DIFFRACTIONr_scbond_it3.15531845
X-RAY DIFFRACTIONr_scangle_it4.7524.51648
LS refinement shellResolution: 2.23→2.287 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 141 -
Rwork0.242 2628 -
all-2769 -
obs--99.71 %

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