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- PDB-5nri: Crystal structure of Burkholderia pseudomallei D-alanine-D-alanin... -

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Basic information

Entry
Database: PDB / ID: 5nri
TitleCrystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP and D-Ala-D-Ala
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / complex
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 / cytosol
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, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / D-ALANINE / TRIETHYLENE GLYCOL / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDiaz-Saez, L. / Hunter, W.N.
CitationJournal: Febs J. / Year: 2019
Title: Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target.
Authors: Diaz-Saez, L. / Torrie, L.S. / McElroy, S.P. / Gray, D. / Hunter, W.N.
History
DepositionApr 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 1, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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
B: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,59019
Polymers66,7582
Non-polymers1,83217
Water14,214789
1
A: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2119
Polymers33,3791
Non-polymers8328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,37910
Polymers33,3791
Non-polymers1,0009
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.642, 61.133, 69.972
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 33378.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: ddl, BURPS1106A_3548 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3NZL3, D-alanine-D-alanine ligase

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Non-polymers , 7 types, 806 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.05 to 0.3 M Li2SO4, 0.1 M Bis-Tris pH 5.5 and 15-30% (w/v) PEG 3350, ratio protein:reservoir 1:1

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.5→69.97 Å / Num. obs: 90609 / % possible obs: 96.6 % / Redundancy: 3.1 % / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: see publication

Resolution: 1.5→69.97 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.339 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20767 4448 4.9 %RANDOM
Rwork0.13253 ---
obs0.13616 86139 96.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.004 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å2-1.4 Å2
2--0.86 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.5→69.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 115 789 5582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0195073
X-RAY DIFFRACTIONr_bond_other_d0.0020.024847
X-RAY DIFFRACTIONr_angle_refined_deg2.5831.9916878
X-RAY DIFFRACTIONr_angle_other_deg1.432311224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1295627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01123.48227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82415832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8511542
X-RAY DIFFRACTIONr_chiral_restr0.1740.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215607
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021042
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_it5.6522.282500
X-RAY DIFFRACTIONr_mcbond_other5.6522.4212499
X-RAY DIFFRACTIONr_mcangle_it6.7583.4393118
X-RAY DIFFRACTIONr_mcangle_other6.75821.1933119
X-RAY DIFFRACTIONr_scbond_it6.6832.6112573
X-RAY DIFFRACTIONr_scbond_other6.6792.6112573
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.683.7783752
X-RAY DIFFRACTIONr_long_range_B_refined8.43530.1135917
X-RAY DIFFRACTIONr_long_range_B_other8.43530.1175918
X-RAY DIFFRACTIONr_rigid_bond_restr4.98439919
X-RAY DIFFRACTIONr_sphericity_free39.1215512
X-RAY DIFFRACTIONr_sphericity_bonded21.439510098
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 351 -
Rwork0.218 6411 -
obs--98.11 %

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