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- PDB-5dmx: Crystal structure of D-alanine-D-alanine ligase from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 5dmx
TitleCrystal structure of D-alanine-D-alanine ligase from Acinetobacter baumannii, space group p212121
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / D-alanine-D-alanine ligase / Acinetobacter baumannii / drug target protein / apo structure
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 / 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 speciesAcinetobacter baumannii ACICU (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsHuynh, K.H. / Hong, M.K. / Kang, L.W.
CitationJournal: J. Microbiol. / Year: 2015
Title: The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding
Authors: Huynh, K.H. / Hong, M.K. / Lee, C. / Tran, H.T. / Lee, S.H. / Ahn, Y.J. / Cha, S.S. / Kang, L.W.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase
E: D-alanine--D-alanine ligase
F: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)200,3566
Polymers200,3566
Non-polymers00
Water1,24369
1
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)66,7852
Polymers66,7852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-17 kcal/mol
Surface area21490 Å2
MethodPISA
2
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)66,7852
Polymers66,7852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-17 kcal/mol
Surface area22990 Å2
MethodPISA
3
E: D-alanine--D-alanine ligase
F: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)66,7852
Polymers66,7852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-17 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.677, 116.779, 177.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33392.746 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ACICU (bacteria)
Strain: ACICU / Gene: ddl, ACICU_03532 / Production host: Escherichia coli (E. coli) / References: UniProt: B2I1J3, D-alanine-D-alanine ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06 M MgCl2, CaCl2, 0.1 M imidazole, MES-HCl, 30% EDO-P8K, 40%(v/v) ethylene glycol, 20%(w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 55982 / % possible obs: 96 % / Redundancy: 7.4 % / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.6 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v4z

3v4z


Resolution: 2.81→44.82 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.887 / SU B: 18.66 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.75 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 2915 5.1 %RANDOM
Rwork0.2478 ---
obs0.2501 54678 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 211.91 Å2 / Biso mean: 89.222 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å2-0 Å2
2---3.73 Å20 Å2
3---4.59 Å2
Refinement stepCycle: final / Resolution: 2.81→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11093 0 0 69 11162
Biso mean---67.13 -
Num. residues----1460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911277
X-RAY DIFFRACTIONr_bond_other_d0.0080.0210980
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.96415252
X-RAY DIFFRACTIONr_angle_other_deg1.696325248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76751436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88125.011473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.327151925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9731558
X-RAY DIFFRACTIONr_chiral_restr0.1070.21748
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212719
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022431
X-RAY DIFFRACTIONr_mcbond_it6.9058.6375816
X-RAY DIFFRACTIONr_mcbond_other6.9048.6365815
X-RAY DIFFRACTIONr_mcangle_it10.48712.9317228
LS refinement shellResolution: 2.812→2.885 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 201 -
Rwork0.375 3845 -
all-4046 -
obs--96.43 %

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