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- PDB-4eg0: Crystal Structure of D-alanine--D-alanine ligase from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 4eg0
TitleCrystal Structure of D-alanine--D-alanine ligase from Burkholderia ambifaria
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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, B domain / 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 speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 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 / 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 / _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
B: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7657
Polymers67,4542
Non-polymers3105
Water6,972387
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-6 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.380, 118.110, 56.930
Angle α, β, γ (deg.)90.000, 91.560, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

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


Mass: 33727.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: ddl, BamMC406_0490 / Production host: Escherichia coli (E. coli) / References: UniProt: B1YSS6, D-alanine-D-alanine ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus condition A12: 0.06 M magnesium chloride, 0.06 M calcium chloride, 0.1 M TRIS-Bicine, 37.5% MPD/PEG1000/PEG3350, 20.26 mg/ml BuamA.00119.a.A1 PS01236, pH 8.5, VAPOR DIFFUSION, ...Details: Morpheus condition A12: 0.06 M magnesium chloride, 0.06 M calcium chloride, 0.1 M TRIS-Bicine, 37.5% MPD/PEG1000/PEG3350, 20.26 mg/ml BuamA.00119.a.A1 PS01236, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 76670 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.182 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 17.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.690.4782.2914782554297.9
1.69-1.740.3553.0614515540097.7
1.74-1.790.2673.9814219526497.5
1.79-1.840.2264.6913758508197.5
1.84-1.910.1716.2112996483296.2
1.91-1.970.1238.3912709468596.4
1.97-2.050.09410.5612598458996.4
2.05-2.130.07213.5111736428995.7
2.13-2.220.05616.6111581417895.4
2.22-2.330.04719.7710847390494.5
2.33-2.460.03922.7810547376894.4
2.46-2.610.03525.629888350893.8
2.61-2.790.02929.449300328293.5
2.79-3.010.02733.588619304492.4
3.01-3.30.02338.17810275891.8
3.3-3.690.02243.17056248690.6
3.69-4.260.02245.976134218590.6
4.26-5.220.0248.685457185090.1
5.22-7.380.02148.84260141088.8
7.380.01850.71204670579.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IOV

1iov


Resolution: 1.65→40.978 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8723 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 3840 5.02 %RANDOM
Rwork0.1733 ---
obs0.1747 76559 99.87 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.279 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 90.24 Å2 / Biso mean: 31.1757 Å2 / Biso min: 10.71 Å2
Baniso -1Baniso -2Baniso -3
1-6.1947 Å2-0 Å2-1.6442 Å2
2---6.1428 Å20 Å2
3----0.0519 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 20 387 4678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184448
X-RAY DIFFRACTIONf_angle_d1.746058
X-RAY DIFFRACTIONf_chiral_restr0.131697
X-RAY DIFFRACTIONf_plane_restr0.009797
X-RAY DIFFRACTIONf_dihedral_angle_d12.5771601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.67080.29781500.276127562906100
1.6708-1.69280.2821360.256826222758100
1.6928-1.71590.28561390.253527122851100
1.7159-1.74050.23741300.216326942824100
1.7405-1.76640.27121370.219826812818100
1.7664-1.7940.22851350.21127292864100
1.794-1.82350.24231490.207426472796100
1.8235-1.85490.261480.215127012849100
1.8549-1.88860.23361490.185627072856100
1.8886-1.9250.22761310.183126662797100
1.925-1.96420.22381320.172126852817100
1.9642-2.0070.2221500.177826852835100
2.007-2.05360.19911210.174627272848100
2.0536-2.1050.19511480.168727112859100
2.105-2.16190.19941330.166826662799100
2.1619-2.22550.20851500.173326832833100
2.2255-2.29730.21721360.160626942830100
2.2973-2.37940.19651450.171226922837100
2.3794-2.47470.18321420.169926852827100
2.4747-2.58730.20231450.167227002845100
2.5873-2.72370.20831460.17126902836100
2.7237-2.89430.18891430.177426862829100
2.8943-3.11770.20161270.183627102837100
3.1177-3.43130.19011660.175626832849100
3.4313-3.92750.1941720.157426812853100
3.9275-4.94690.15941420.138727282870100
4.9469-40.9780.18951380.17532698283698
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)
15.16770.0757-0.40573.6227-0.40462.7681-0.0973-0.533-0.09840.92840.1043-0.01290.1223-0.169-0.02220.41090.00460.03940.1905-0.02260.13458.872119.650435.1807
21.0264-0.5283-0.30890.94050.67061.7065-0.1514-0.1267-0.08140.23110.05620.07610.20840.15280.09280.14950.01350.01280.11730.01480.161718.588411.899618.692
35.15350.51871.87643.8370.24582.74550.3565-0.0858-0.37760.3551-0.1733-0.42130.2103-0.0403-0.15810.1092-0.0301-0.03210.23370.02220.288439.334918.11088.819
41.1329-0.3263-1.81712.8727-0.35243.82190.1006-0.04620.2089-0.0380.00960.1086-0.2821-0.0126-0.09910.07820.0004-0.01880.11870.00570.143315.156830.217.4168
51.39510.0896-1.26181.4311-0.62233.47790.0364-0.00690.04620.136-0.03030.214-0.2319-0.19980.01140.08670.0092-0.00090.1344-0.0110.155211.508722.885413.7283
63.4961-0.28640.8794.07140.8424.7198-0.2088-0.56760.12350.71530.14020.1706-0.36270.26670.07790.43710.0525-0.02720.16180.00260.171728.4035-7.314336.4414
70.7484-1.62760.1883.9479-0.05220.3659-0.4003-0.393-0.08851.12630.34480.6103-0.2937-0.166-0.04190.53170.10830.10260.25950.06440.245723.2645-9.77538.2643
80.8358-0.1634-0.16720.8813-0.38932.3193-0.072-0.1170.01280.33480.0794-0.1007-0.1559-0.0745-0.00510.23580.0307-0.01340.1063-0.00630.127722.6637-0.312221.5891
90.51710.31590.25422.8949-0.24682.93240.21250.2421-0.0588-0.1356-0.20731.50020.0347-1.2976-0.04870.1640.024-0.08710.4659-0.10950.55947.8102-6.56960.6447
100.958-0.60210.24012.59870.54613.62690.0005-0.0281-0.10110.1808-0.0213-0.03040.1995-0.01990.00270.1141-0.01280.00290.11370.00630.11930.2011-14.82814.3651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:64)A4 - 64
2X-RAY DIFFRACTION2(chain A and resid 65:121)A65 - 121
3X-RAY DIFFRACTION3(chain A and resid 122:184)A122 - 184
4X-RAY DIFFRACTION4(chain A and resid 185:240)A185 - 240
5X-RAY DIFFRACTION5(chain A and resid 241:311)A241 - 311
6X-RAY DIFFRACTION6(chain B and resid 4:21)B4 - 21
7X-RAY DIFFRACTION7(chain B and resid 22:62)B22 - 62
8X-RAY DIFFRACTION8(chain B and resid 63:117)B63 - 117
9X-RAY DIFFRACTION9(chain B and resid 118:185)B118 - 185
10X-RAY DIFFRACTION10(chain B and resid 186:311)B186 - 311

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