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- PDB-3tqt: Structure of the D-alanine-D-alanine ligase from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tqt
TitleStructure of the D-alanine-D-alanine ligase from Coxiella burnetii
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / Cell envelope
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, 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
D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsRudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)82,5302
Polymers82,5302
Non-polymers00
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-33 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.238, 97.442, 106.563
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: 41265.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: ddl, CBU_1338 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83BZ9, D-alanine-D-alanine ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 293 K / Method: sitting drop / pH: 6
Details: 100 mM MES pH 6.0, 5% PEG 3350, 30% PEG 200, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 58072 / Num. obs: 56853 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.043 / Χ2: 0.923 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.88-1.9340.37926980.55194.9
1.93-1.974.10.30227530.57195
1.97-2.014.10.2427190.599196.1
2.01-2.054.20.20227840.599197.5
2.05-2.094.20.16527770.646196.5
2.09-2.144.30.14728060.675197.5
2.14-2.194.40.12628390.706198.6
2.19-2.254.50.10828050.725198.5
2.25-2.324.70.10428500.772198.4
2.32-2.394.80.08428350.801198.7
2.39-2.484.90.07728530.825198.9
2.48-2.5850.07128350.871199
2.58-2.75.10.06228810.91199.2
2.7-2.845.10.05328810.958199.3
2.84-3.025.20.04528831.059198.9
3.02-3.255.10.03929111.222199.6
3.25-3.585.10.03429111.335199.4
3.58-4.095.10.03129301.367199.4
4.09-5.1650.02729671.341199.7
5.16-504.70.02829351.317193.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→39.652 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8452 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 2875 5.06 %
Rwork0.1804 --
all0.1826 59669 -
obs0.1826 56794 96.74 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.038 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 105.05 Å2 / Biso mean: 33.2752 Å2 / Biso min: 13.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.8371 Å2-0 Å20 Å2
2---6.0247 Å20 Å2
3---3.1876 Å2
Refinement stepCycle: LAST / Resolution: 1.88→39.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5340 0 0 490 5830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065442
X-RAY DIFFRACTIONf_angle_d1.0557379
X-RAY DIFFRACTIONf_chiral_restr0.068856
X-RAY DIFFRACTIONf_plane_restr0.005942
X-RAY DIFFRACTIONf_dihedral_angle_d14.2692011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.94480.28922410.21864595483683
1.9448-2.02270.25262830.195306558996
2.0227-2.11480.24732910.18345348563997
2.1148-2.22620.24652980.17985404570298
2.2262-2.36570.2482800.18255469574999
2.3657-2.54830.24883150.18985453576899
2.5483-2.80470.23382910.19815524581599
2.8047-3.21040.23712830.18735559584299
3.2104-4.04410.21163110.16815593590499
4.0441-39.66030.18592820.17125668595097
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0631-0.5555-0.09450.7483-0.01811.67630.0997-0.0943-0.1230.2549-0.03890.0340.027-0.078-0.04360.2503-0.0587-0.07920.15620.02360.198664.189162.5449-8.4817
21.6804-0.04930.00890.5175-0.27580.14030.06440.0549-0.2601-0.0566-0.15080.00930.0211-0.04690.02930.18750.0038-0.02790.1735-0.04870.184753.601743.6705-32.7004
31.8636-0.0519-0.10770.57010.11310.8777-0.0198-0.0347-0.53650.1841-0.1693-0.13990.0936-0.00970.04710.2226-0.015-0.02940.17360.00060.356853.014634.2665-26.096
40.7125-0.2843-0.14391.61640.36120.9713-0.00040.0206-0.1178-0.03770.0021-0.41850.050.11310.01720.1660.0061-0.03050.17730.00560.266773.376750.2066-27.9039
51.0132-0.28030.12580.7925-0.15140.46580.0247-0.28270.64690.2101-0.0068-0.2437-0.2061-0.130.03630.2640.0181-0.03060.1982-0.02440.273756.685479.2236-30.7631
61.0151-0.83350.06512.50410.28841.27220.0327-0.09950.09730.1734-0.0030.0371-0.2094-0.0514-0.01810.1890.02650.04360.20890.00550.186738.510873.6549-13.5424
70.86190.0637-0.3661.12080.39610.92330.10660.0102-0.0251-0.1817-0.02730.113-0.3040.0967-0.1130.17010.0361-0.03820.1928-0.01540.159946.762660.2825-28.272
81.39250.33840.10161.6706-0.05490.6043-0.06210.50620.0532-0.53910.1263-0.0833-0.11710.1184-0.0620.3374-0.01650.00950.3315-0.00610.143956.428470.1618-47.4729
91.3238-0.0380.59221.52660.16120.84770.0940.1942-0.0863-0.34150.04370.34940.02720.0457-0.02140.30020.0417-0.14190.2648-0.02510.232235.860258.4658-40.6552
100.53990.2538-0.18241.75220.11611.32670.11030.0061-0.19380.0059-0.06980.54380.1663-0.1844-0.02250.1803-0.0132-0.01080.20240.00470.243235.004856.5621-22.2608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:132)A2 - 132
2X-RAY DIFFRACTION2(chain A and resid 133:172)A133 - 172
3X-RAY DIFFRACTION3(chain A and resid 173:224)A173 - 224
4X-RAY DIFFRACTION4(chain A and resid 225:355)A225 - 355
5X-RAY DIFFRACTION5(chain A and resid 356:371)A356 - 371
6X-RAY DIFFRACTION6(chain B and resid 4:99)B4 - 99
7X-RAY DIFFRACTION7(chain B and resid 100:158)B100 - 158
8X-RAY DIFFRACTION8(chain B and resid 159:224)B159 - 224
9X-RAY DIFFRACTION9(chain B and resid 225:320)B225 - 320
10X-RAY DIFFRACTION10(chain B and resid 321:368)B321 - 368

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