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

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Basic information

Entry
Database: PDB / ID: 5nrh
TitleCrystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP
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 / 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, 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--D-alanine ligase / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDiaz-Saez, L. / Hunter, W.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Defence Sciecne and Technology Laboratory United Kingdom
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,85510
Polymers66,7582
Non-polymers1,0978
Water14,142785
1
A: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0337
Polymers33,3791
Non-polymers6546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8223
Polymers33,3791
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.648, 61.150, 70.079
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 311
2010B4 - 311

NCS ensembles :
ID
1
2

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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, UniProt: Q63QJ9*PLUS, D-alanine-D-alanine ligase

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Non-polymers , 5 types, 793 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
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: 1.3→70.08 Å / Num. obs: 141049 / % possible obs: 97.6 % / Redundancy: 4.8 % / Net I/σ(I): 15

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Processing

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

Resolution: 1.3→70.08 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.286 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.053
RfactorNum. reflection% reflectionSelection details
Rfree0.19007 7097 5 %RANDOM
Rwork0.14591 ---
obs0.14825 133936 97.58 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 24.763 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å21.52 Å2
2--0.64 Å20 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.3→70.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 69 785 5526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195124
X-RAY DIFFRACTIONr_bond_other_d0.0020.024908
X-RAY DIFFRACTIONr_angle_refined_deg2.2471.9896976
X-RAY DIFFRACTIONr_angle_other_deg1.4443.00311383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7115648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34123.348233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80215859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5231545
X-RAY DIFFRACTIONr_chiral_restr0.1840.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215695
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021060
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_it3.7262.2252518
X-RAY DIFFRACTIONr_mcbond_other3.7162.2222517
X-RAY DIFFRACTIONr_mcangle_it4.5813.3573154
X-RAY DIFFRACTIONr_mcangle_other4.5833.3593155
X-RAY DIFFRACTIONr_scbond_it5.3852.4252606
X-RAY DIFFRACTIONr_scbond_other5.3862.4252607
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2533.5433807
X-RAY DIFFRACTIONr_long_range_B_refined7.27728.8855971
X-RAY DIFFRACTIONr_long_range_B_other7.27628.8875972
X-RAY DIFFRACTIONr_rigid_bond_restr4.711310032
X-RAY DIFFRACTIONr_sphericity_free42.4265497
X-RAY DIFFRACTIONr_sphericity_bonded19.534510205
Refine LS restraints NCS

Ens-ID: 1 / Number: 18826 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 482 -
Rwork0.232 9734 -
obs--95.93 %

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