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- PDB-4egj: Crystal structure of D-alanine-D-alanine ligase from Burkholderia... -

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Basic information

Entry
Database: PDB / ID: 4egj
TitleCrystal structure of D-alanine-D-alanine ligase from Burkholderia xenovorans
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / D-alanine-D-alanine ligase
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, 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 speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSSGCID / Seattle 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 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)143,4434
Polymers143,4434
Non-polymers00
Water6,449358
1
A: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)35,8611
Polymers35,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)35,8611
Polymers35,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)35,8611
Polymers35,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)35,8611
Polymers35,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: D-alanine--D-alanine ligase

C: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)71,7222
Polymers71,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-y+1,x,z-1/41
Buried area2230 Å2
ΔGint-18 kcal/mol
Surface area23420 Å2
MethodPISA
6
B: D-alanine--D-alanine ligase

D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)71,7222
Polymers71,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-y+1,x,z-1/41
Buried area2180 Å2
ΔGint-19 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.930, 78.930, 224.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA4 - 31125 - 332
21LEULEUBB4 - 31125 - 332
12LEULEUAA4 - 31125 - 332
22LEULEUCC4 - 31125 - 332
13LEULEUAA4 - 31125 - 332
23LEULEUDD4 - 31125 - 332
14LEULEUBB4 - 31125 - 332
24LEULEUCC4 - 31125 - 332
15LEULEUBB4 - 31125 - 332
25LEULEUDD4 - 31125 - 332
16LYSLYSCC4 - 31225 - 333
26LYSLYSDD4 - 31225 - 333

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 35860.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: Bxeno_A3907, Bxe_A0488, ddl / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13TZ4, D-alanine-D-alanine ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Qiagen JCSG Core1 screen d5: 20% PEG 3350, 200mM LiCl; BuxeA.00119.a.A1 PS01358 at 23.2mg/ml, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 22, 2012
RadiationMonochromator: RIGAKU VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 60791 / Num. obs: 59426 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 36.882 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsRsym value% possible all
2.3-2.362.40.4782.0910794446344330.47899.3
2.36-2.420.3392.9510830437799.4
2.42-2.490.2653.610460421999.5
2.49-2.570.2483.8210229412699.7
2.57-2.660.2284.319931398599.6
2.66-2.750.1935.049601384399.2
2.75-2.850.165.869375373499.8
2.85-2.970.1297.088973357399.7
2.97-3.10.1018.718714346699.7
3.1-3.250.08110.68252326399.6
3.25-3.430.0712.497917314199.4
3.43-3.640.06414.237093285596.9
3.64-3.890.06118.046068251490.3
3.89-4.20.04420.346249251195.7
4.2-4.60.03624.835653229395.5
4.6-5.140.03524.675090203794.7
5.14-5.940.03920.794616183295
5.94-7.270.03819.983845150292.8
7.27-10.290.02227.12875112088.5
10.290.01728.36158760284.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å44.76 Å
Translation2.5 Å44.76 Å

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Processing

Software
NameVersionClassification
JDirectordata collection
PHASERphasing
REFMAC5.6.0117refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3eg0

3eg0


Resolution: 2.3→49.99 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.2318 / WRfactor Rwork: 0.2012 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.828 / SU B: 13.316 / SU ML: 0.166 / SU R Cruickshank DPI: 0.3216 / SU Rfree: 0.2367 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 3006 5.1 %RANDOM
Rwork0.2236 ---
all0.2254 60791 --
obs0.2254 59384 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.63 Å2 / Biso mean: 32.5859 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å2-0 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8047 0 0 358 8405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198230
X-RAY DIFFRACTIONr_bond_other_d0.0080.025445
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.98211205
X-RAY DIFFRACTIONr_angle_other_deg1.473313270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9451095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94423.686331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.747151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5671557
X-RAY DIFFRACTIONr_chiral_restr0.0950.21285
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219403
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021670
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)
11A963610.07
12B963620.07
21A885130.09
22C885140.09
31A822450.09
32D822460.09
41B871570.09
42C871580.09
51B820290.1
52D8202100.1
61C8282110.08
62D8282120.08
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 255 -
Rwork0.332 4111 -
all-4366 -
obs-4433 99.25 %
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)
10.6211-0.46470.18831.2909-0.41970.7487-0.03440.0702-0.04920.1383-0.02040.04050.020.01880.05480.247-0.03210.04450.18570.04080.033317.14459.0043.477
20.7679-0.7561-0.12951.6402-0.08440.8753-0.02250.0135-0.07580.1067-0.02750.07980.01190.00680.050.2251-0.0330.03320.19520.03120.020416.40458.492115.098
31.27160.64050.14370.91670.36521.46810.0013-0.0789-0.0404-0.0454-0.0276-0.023-0.02050.03510.02640.31920.06770.05490.154-0.02220.022168.25150.96432.903
40.94570.73320.12210.8710.40451.12440.0264-0.0558-0.0097-0.0625-0.10120.01290.0699-0.00470.07470.27440.03570.04560.1561-0.02490.018467.32352.38143.874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 311
2X-RAY DIFFRACTION1A401 - 513
3X-RAY DIFFRACTION2B4 - 311
4X-RAY DIFFRACTION2B401 - 498
5X-RAY DIFFRACTION3C4 - 312
6X-RAY DIFFRACTION3C401 - 469
7X-RAY DIFFRACTION4D3 - 312
8X-RAY DIFFRACTION4D401 - 478

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