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- PDB-2yzg: Crystal structure of D-ALA:D-ALA Ligase from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2yzg
TitleCrystal structure of D-ALA:D-ALA Ligase from Thermus thermophilus HB8
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / D-alanine:D-alanine ligase / Cell shape / 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
D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKitamura, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of D-ALA:D-ALA Ligase from Thermus thermophilus HB8
Authors: Kitamura, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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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
C: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)104,6623
Polymers104,6623
Non-polymers00
Water3,675204
1
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)69,7752
Polymers69,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2745.5 Å2
MethodPISA
2
C: D-alanine--D-alanine ligase

C: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)69,7752
Polymers69,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2742.9 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.224, 56.412, 142.213
Angle α, β, γ (deg.)90.00, 109.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34887.395 Da / Num. of mol.: 3
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) / References: UniProt: Q5SHZ3, D-alanine-D-alanine ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 14% PEG4000, 0.1M Na Chloride, 0.1M MES, pH 5.8, 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: 0.979029, 0.900000, 0.97924
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 3, 2005
RadiationMonochromator: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790291
20.91
30.979241
ReflectionResolution: 2.3→50 Å / Num. obs: 54945 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 25.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.2 / Num. unique all: 5452 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→44.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 99904.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 5414 10.2 %RANDOM
Rwork0.243 ---
obs0.243 53311 96.4 %-
all-54945 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.481 Å2 / ksol: 0.321381 e/Å3
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å23.17 Å2
2--2.98 Å20 Å2
3----4.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7189 0 0 204 7393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 759 9.5 %
Rwork0.299 7232 -
obs--87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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