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- PDB-4me6: Crystal structure of D-alanine-D-alanine ligase A from Xanthomona... -

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Basic information

Entry
Database: PDB / ID: 4me6
TitleCrystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / ADP-depending enzyme / d-alanine-d-alanine ligase / Nucleotide binding
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, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / 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, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / 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
ADENOSINE-5'-DIPHOSPHATE / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDoan, T.T.N. / Kim, J.K. / Ahn, Y.J. / Lee, B.M. / Kang, L.W.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides
Authors: Doan, T.N.N. / Kim, J.K. / Ngo, H.P.T. / Tran, H.T. / Cha, S.S. / Chung, K.M. / Huynh, K.H. / Ahn, Y.J. / Kang, L.W.
History
DepositionAug 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3973
Polymers41,9461
Non-polymers4522
Water3,081171
1
A: D-alanine--D-alanine ligase
hetero molecules

A: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7956
Polymers83,8922
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5850 Å2
ΔGint-59 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.236, 83.236, 98.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 41945.777 Da / Num. of mol.: 1 / Mutation: M327V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KACC10331 / Gene: ddlA, ddl, XOO0352 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H614, D-alanine-D-alanine ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-21 ARE PART OF THE MATURE PROTEIN ACCORDING TO DATABASE GI:122879012 (PROTEIN REF YP_198991.6).

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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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% (w/v) PEG 4000, 0.1M Tris (pH 8.5), 0.2M MgCl2, 0.3M dimethylethyl-(3-sulfopropyl)-ammonium, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20817 / % possible obs: 99.5 %
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 8.9 / Rsym value: 0.61 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E5N

3e5n


Resolution: 2.1→38.32 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.619 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25068 1981 9.7 %RANDOM
Rwork0.19201 ---
obs0.1976 18463 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 28 171 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192618
X-RAY DIFFRACTIONr_bond_other_d0.0010.022586
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9753558
X-RAY DIFFRACTIONr_angle_other_deg0.83635896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38723.707116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78815422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5691523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
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_it2.12.3451343
X-RAY DIFFRACTIONr_mcbond_other2.0852.3431342
X-RAY DIFFRACTIONr_mcangle_it3.2453.4941670
X-RAY DIFFRACTIONr_mcangle_other4.4035.3861712
X-RAY DIFFRACTIONr_scbond_it2.9442.8571275
X-RAY DIFFRACTIONr_scbond_other3.9614.1161238
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0846.0161849
X-RAY DIFFRACTIONr_long_range_B_refined8.08529.1822871
X-RAY DIFFRACTIONr_long_range_B_other8.08129.1632858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 137 -
Rwork0.244 1282 -
obs--95.94 %

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