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- PDB-5d8d: Crystal structure of D-alanine-D-alanine ligase from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 5d8d
TitleCrystal structure of D-alanine-D-alanine ligase from Acinetobacter baumannii
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / D-alanine-D-alanine ligase / Acinetobacter baumannii / Apo structure / Drug target
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: 2.19 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
DepositionAug 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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
Water3,585199
1
A: D-alanine--D-alanine ligase
C: 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-16 kcal/mol
Surface area23320 Å2
MethodPISA
2
B: D-alanine--D-alanine ligase
E: 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 area2700 Å2
ΔGint-18 kcal/mol
Surface area23600 Å2
MethodPISA
3
D: 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 area2270 Å2
ΔGint-14 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.618, 74.766, 143.117
Angle α, β, γ (deg.)90.00, 103.27, 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 / 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.: 199 / 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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 287 K / Method: microbatch / pH: 6.9 / Details: 0.2M NaSCN, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 115881 / % possible obs: 99.6 % / Redundancy: 5.2 % / Net I/σ(I): 22.1
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 99

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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 / Resolution: 2.19→36.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.406 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28065 5778 5 %RANDOM
Rwork0.22062 ---
obs0.22365 109440 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2---0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.19→36.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12711 0 0 199 12910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912909
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212523
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.95917465
X-RAY DIFFRACTIONr_angle_other_deg1.111328826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0951655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24625.312544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.68152211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.981560
X-RAY DIFFRACTIONr_chiral_restr0.1210.22005
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214618
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022758
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6186.1996683
X-RAY DIFFRACTIONr_mcbond_other4.6176.1996682
X-RAY DIFFRACTIONr_mcangle_it6.9079.2678317
X-RAY DIFFRACTIONr_mcangle_other6.9079.2678318
X-RAY DIFFRACTIONr_scbond_it4.8476.7366226
X-RAY DIFFRACTIONr_scbond_other4.8466.7376227
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4999.8989149
X-RAY DIFFRACTIONr_long_range_B_refined10.1548.49613861
X-RAY DIFFRACTIONr_long_range_B_other10.14548.48913854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.193→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 360 -
Rwork0.4 7098 -
obs--86.99 %

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