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- PDB-2zdq: Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Al... -

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Basic information

Entry
Database: PDB / ID: 2zdq
TitleCrystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from Thermus thermophius HB8
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / D-Alanine-D-Alanine Ligase / Peptidoglycan Biosynthesis / Cell shape / Cell wall biogenesis/degradation / Peptidoglycan synthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
ADENOSINE-5'-TRIPHOSPHATE / D-ALANINE / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKitamuta, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from Thermus thermophius HB8
Authors: Kitamura, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionNov 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,7708
Polymers69,4002
Non-polymers1,3716
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-21 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.052, 95.052, 192.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein D-alanine--D-alanine ligase


Mass: 34699.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHZ3, D-alanine-D-alanine ligase
#2: Chemical
ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUES A 401-402 AND B 403-404 FORM TWO DIPEPTIDE SUBSTRATES BOUND TO THE ENZYME

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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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.91M K2 H Phosphate, 0.49M Na H2 Phosphate, 20% Glycerol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2007
Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 39948 / Num. obs: 39771 / % possible obs: 99.6 % / Redundancy: 17.3 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.07 / Net I/σ(I): 34.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.65 / Num. unique all: 3776 / Rsym value: 0.326 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZDG

2zdg


Resolution: 2.3→48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 68875.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3828 10.1 %RANDOM
Rwork0.231 ---
obs0.231 37945 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.1816 Å2 / ksol: 0.331428 e/Å3
Displacement parametersBiso mean: 41.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.17 Å20 Å20 Å2
2--7.17 Å20 Å2
3----14.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 84 194 5184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d3.7
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 579 10.3 %
Rwork0.335 5025 -
obs--85.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein2.paramprotein2.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3atp_xplor.paramatp_xplor.top

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