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- PDB-2fb9: Crystal structure of the Apo form of D-alanine: D-alanine ligase ... -

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Basic information

Entry
Database: PDB / ID: 2fb9
TitleCrystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes
ComponentsD-alanine:D-alanine ligase
KeywordsLIGASE
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 speciesThermus caldophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLee, J.H. / Na, Y. / Eom, S.H.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: A basis for the substrate-induced conformational changes
Authors: Lee, J.H. / Na, Y. / Song, H.E. / Kim, D. / Park, B.H. / Rho, S.H. / Im, Y.J. / Kim, M.K. / Kang, G.B. / Lee, D.S. / Eom, S.H.
History
DepositionDec 8, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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


Theoretical massNumber of molelcules
Total (without water)35,1071
Polymers35,1071
Non-polymers00
Water2,072115
1
A: D-alanine:D-alanine ligase

A: D-alanine:D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)70,2152
Polymers70,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area27930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.216, 132.744, 59.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsBiological unit is dimer

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Components

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


Mass: 35107.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus caldophilus (bacteria) / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3T920, D-alanine-D-alanine ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 29%(w/v) PEG MME 2000, 0.1M Tris-HCl, 0.2M Sodium Acetate, 0.2M KSCN, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25640 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.96 Å / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 3379 RANDOM
Rwork0.228 --
all0.249 33979 -
obs0.232 24867 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 0 115 2596

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