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- PDB-2i87: Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanin... -

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Basic information

Entry
Database: PDB / ID: 2i87
TitleAllosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies
ComponentsD-alanine-D-alanine ligase
KeywordsLIGASE / d-alanine:d-alanine ligase / apo
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, 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 speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, S. / Chang, J.S. / Herberg, J.T. / Horng, M. / Tomich, P.K. / Lin, A.H. / Marotti, K.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies.
Authors: Liu, S. / Chang, J.S. / Herberg, J.T. / Horng, M.M. / Tomich, P.K. / Lin, A.H. / Marotti, K.R.
History
DepositionSep 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Apr 15, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)82,8894
Polymers82,6972
Non-polymers1922
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-36 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.661, 66.408, 78.590
Angle α, β, γ (deg.)90.00, 96.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41348.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: COL / Gene: ddl / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q5HEB7, D-alanine-D-alanine ligase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.12 Å3/Da / Density % sol: 42.03 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2001 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→79 Å / Num. all: 46823 / Num. obs: 46823 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 37.8 Å2 / Rsym value: 0.038 / Net I/σ(I): 26.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 3276 / Rsym value: 0.162 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.3.0008 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1EHI

1ehi


Resolution: 2→79.06 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.699 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24148 2336 5 %RANDOM
Rwork0.1998 ---
obs0.20187 44470 99.62 %-
all-46823 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.837 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.01 Å2
2--0.27 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5479 0 10 91 5580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225593
X-RAY DIFFRACTIONr_bond_other_d0.0010.023746
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9677567
X-RAY DIFFRACTIONr_angle_other_deg1.03439214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.335683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44825.957277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.746151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4571518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021033
X-RAY DIFFRACTIONr_nbd_refined0.230.21276
X-RAY DIFFRACTIONr_nbd_other0.2060.24000
X-RAY DIFFRACTIONr_nbtor_refined0.1940.22750
X-RAY DIFFRACTIONr_nbtor_other0.0970.23100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5671.54305
X-RAY DIFFRACTIONr_mcbond_other0.3571.51388
X-RAY DIFFRACTIONr_mcangle_it1.93325534
X-RAY DIFFRACTIONr_scbond_it3.07432471
X-RAY DIFFRACTIONr_scangle_it4.2564.52033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 181 -
Rwork0.188 3276 -
obs--99.63 %
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)
12.81760.096-1.13141.0428-0.5413.8172-0.08080.2836-0.178-0.1294-0.0572-0.12730.3010.10690.138-0.09120.00010.0216-0.01830.0125-0.066526.10950.0007-5.1906
22.7842-0.75071.08211.9108-0.88952.38110.1414-0.0567-0.2658-0.05810.08180.12480.5534-0.3375-0.22320.029-0.1019-0.0025-0.0949-0.0197-0.057710.0311-16.972820.921
32.33431.2442-0.32591.9984-0.02091.63770.02380.17530.1533-0.05690.010.2097-0.0641-0.2265-0.0338-0.14320.0095-0.0153-0.03350.0143-0.02025.95841.63383.1506
43.47220.01150.48960.85580.91963.1648-0.06180.48330.28370.00970.0337-0.1253-0.36560.63570.0281-0.0702-0.066-0.03380.08220.0996-0.043342.52842.462217.2792
50.7547-1.00820.53912.139-1.20324.3812-0.1099-0.12680.07790.35540.18520.099-0.7323-0.3419-0.07530.06160.06460.0546-0.0774-0.0368-0.011710.950514.915426.2898
61.805-0.3121-0.0871.4840.61521.86050.0029-0.0648-0.02180.2393-0.0528-0.02260.03190.10550.04990.01960.0054-0.0153-0.10350.0104-0.102428.6661-2.678232.9995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1253 - 125
2X-RAY DIFFRACTION2AA126 - 219126 - 219
3X-RAY DIFFRACTION3AA220220
4X-RAY DIFFRACTION4BB3 - 1253 - 125
5X-RAY DIFFRACTION5BB126 - 219126 - 219
6X-RAY DIFFRACTION6BB220 - 360220 - 360

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