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- PDB-6ll9: Crystal structure of D-alanine-D-alanine ligase from Aeromonas hy... -

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Basic information

Entry
Database: PDB / ID: 6ll9
TitleCrystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / Aeromonas hydrophila / D-alanine-D-alanine ligase / cell wall
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. / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...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. / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
D-ALANINE / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, H.
CitationJournal: J.Agric.Food Chem. / Year: 2020
Title: Insights into the Inhibition ofAeromonas hydrophilad-Alanine-d-Alanine Ligase by Integration of Kinetics and Structural Analysis.
Authors: Zhang, Y. / Gong, S. / Wang, X. / Muhammad, M. / Li, Y. / Meng, S. / Li, Q. / Liu, D. / Zhang, H.
History
DepositionDec 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _software.name
Revision 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)82,6004
Polymers82,4222
Non-polymers1782
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-15 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.996, 93.589, 110.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 67 or (resid 68...
21(chain B and (resid 4 through 20 or (resid 21...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHE(chain A and (resid 4 through 67 or (resid 68...AA4 - 6749 - 112
12ASPASPASPASP(chain A and (resid 4 through 67 or (resid 68...AA68113
13ILEILEDALDAL(chain A and (resid 4 through 67 or (resid 68...AA - C4 - 40049
14ILEILEDALDAL(chain A and (resid 4 through 67 or (resid 68...AA - C4 - 40049
15ILEILEDALDAL(chain A and (resid 4 through 67 or (resid 68...AA - C4 - 40049
16ILEILEDALDAL(chain A and (resid 4 through 67 or (resid 68...AA - C4 - 40049
21ILEILESERSER(chain B and (resid 4 through 20 or (resid 21...BB4 - 2049 - 65
22LEULEULEULEU(chain B and (resid 4 through 20 or (resid 21...BB2166
23ASNASNDALDAL(chain B and (resid 4 through 20 or (resid 21...BB - D3 - 40048

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Components

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


Mass: 41210.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: ddl / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3S8RJF8, UniProt: A0KKW8*PLUS, D-alanine-D-alanine ligase
#2: Chemical ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.95 Å3/Da / Density % sol: 36.93 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (m/v) PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→71.51 Å / Num. obs: 18212 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 23.52
Reflection shellResolution: 2.7→2.8428 Å / Rmerge(I) obs: 0.589 / Num. unique obs: 2340

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DGI

6dgi


Resolution: 2.7→55.406 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 42.57
RfactorNum. reflection% reflection
Rfree0.35 925 5.08 %
Rwork0.2946 --
obs0.2975 18212 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.45 Å2 / Biso mean: 70 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.7→55.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 12 5 4279
Biso mean--68.24 65.09 -
Num. residues----563
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1568X-RAY DIFFRACTION17.37TORSIONAL
12B1568X-RAY DIFFRACTION17.37TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.84240.48941340.3952411100
2.8424-3.02040.4451340.3924241999
3.0204-3.25360.44311270.3495242599
3.2536-3.5810.43631270.3295244099
3.581-4.0990.37841320.29732469100
4.099-5.16370.31521320.24992508100
5.1637-55.4060.27181390.26162615100
Refinement TLS params.Method: refined / Origin x: -18.0509 Å / Origin y: 16.2672 Å / Origin z: -22.5226 Å
111213212223313233
T0.455 Å2-0.0003 Å2-0.0026 Å2-0.4694 Å2-0.0562 Å2--0.9053 Å2
L0.8995 °20.2343 °2-0.6956 °2-1.8852 °2-1.35 °2--1.8899 °2
S0.0143 Å °-0.0935 Å °-0.2676 Å °-0.1558 Å °-0.2264 Å °-0.2081 Å °0.1821 Å °0.1436 Å °0.2059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 400
2X-RAY DIFFRACTION1allB3 - 400
3X-RAY DIFFRACTION1allS1 - 9

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