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- PDB-3bma: Crystal structure of D-alanyl-lipoteichoic acid synthetase from S... -

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Basic information

Entry
Database: PDB / ID: 3bma
TitleCrystal structure of D-alanyl-lipoteichoic acid synthetase from Streptococcus pneumoniae R6
ComponentsD-alanyl-lipoteichoic acid synthetase
KeywordsLIGASE / STRUCTURAL GENOMICS / D-ALANYL-LIPOTEICHOIC ACID BIOSYNTHESIS / PROTEIN STRUCTURE INITIATIVE / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyDltD / D-alanyl-lipoteichoic acid biosynthesis DltD, Firmicutes / DltD protein / lipoteichoic acid biosynthetic process / plasma membrane / Protein DltD
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsPatskovsky, Y. / Sridhar, V. / Bonanno, J.B. / Smith, D. / Rutter, M. / Iizuka, M. / Koss, J. / Bain, K. / Gheyi, T. / Wasserman, S.R. ...Patskovsky, Y. / Sridhar, V. / Bonanno, J.B. / Smith, D. / Rutter, M. / Iizuka, M. / Koss, J. / Bain, K. / Gheyi, T. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of probable D-Alanyl-Lipoteichoic Acid Synthetase from Streptococcus pneumoniae.
Authors: Patskovsky, Y. / Sridhar, V. / Bonanno, J.B. / Smith, D. / Rutter, M. / Iizuka, M. / Koss, J. / Bain, K. / Gheyi, T. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanyl-lipoteichoic acid synthetase
B: D-alanyl-lipoteichoic acid synthetase
C: D-alanyl-lipoteichoic acid synthetase
D: D-alanyl-lipoteichoic acid synthetase
E: D-alanyl-lipoteichoic acid synthetase
F: D-alanyl-lipoteichoic acid synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,26130
Polymers282,9956
Non-polymers2,26624
Water14,322795
1
C: D-alanyl-lipoteichoic acid synthetase
hetero molecules

D: D-alanyl-lipoteichoic acid synthetase
F: D-alanyl-lipoteichoic acid synthetase
hetero molecules

A: D-alanyl-lipoteichoic acid synthetase
B: D-alanyl-lipoteichoic acid synthetase
E: D-alanyl-lipoteichoic acid synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,26130
Polymers282,9956
Non-polymers2,26624
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_546-x,y-1/2,-z+3/21
crystal symmetry operation3_446-x-1,y-1/2,-z+3/21
identity operation1_555x,y,z1
Buried area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.956, 148.064, 208.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLNGLNAA35 - 2187 - 190
21METMETGLNGLNBB35 - 2187 - 190
31METMETGLNGLNCC35 - 2187 - 190
41METMETGLNGLNDD35 - 2187 - 190
51METMETGLNGLNEE35 - 2187 - 190
61METMETGLNGLNFF35 - 2187 - 190
12ALAALAPHEPHEAA238 - 426210 - 398
22ALAALAPHEPHEBB238 - 426210 - 398
32ALAALAPHEPHECC238 - 426210 - 398
42ALAALAPHEPHEDD238 - 426210 - 398
52ALAALAGLUGLUEE238 - 425210 - 397
62ALAALAVALVALFF238 - 423210 - 395

NCS ensembles :
ID
1
2
DetailsAUTHORS STATE THAT THE HOMO-HEXAMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein
D-alanyl-lipoteichoic acid synthetase


Mass: 47165.844 Da / Num. of mol.: 6 / Fragment: Residues 32-427 / Mutation: C217R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: dltD, spr1979 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DN13
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM Bis-Tris pH 5.5, 21% PEG 6000, 200mM Lithium sulfate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 15, 2006
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 138224 / % possible obs: 99.2 % / Observed criterion σ(I): -0.5 / Redundancy: 6.2 % / Biso Wilson estimate: 31.21 Å2 / Rmerge(I) obs: 0.195 / Rsym value: 0.13 / Net I/σ(I): 2.9
Reflection shellResolution: 2.24→2.33 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 0.8 / % possible all: 96.2

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.938 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27133 4142 3 %RANDOM
Rwork0.21393 ---
obs0.21568 132819 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.441 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---1.42 Å20 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.24→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19174 0 130 795 20099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02220056
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.94627128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.08752414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68224.7751068
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.939153472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2141591
X-RAY DIFFRACTIONr_chiral_restr0.0780.22744
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1260.39123
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.513520
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.51575
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0860.3115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.526
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.483212188
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.015319042
X-RAY DIFFRACTIONr_scbond_it5.92139055
X-RAY DIFFRACTIONr_scangle_it8.14958046
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1381tight positional0.520.5
11B1381tight positional0.360
11C1381tight positional0.480
11D1381tight positional0.620
11E1381tight positional0.410
11F1381tight positional0.430
22A1486tight positional0.480.5
22B1486tight positional0.470
22C1486tight positional0.560
22D1486tight positional0.590
22E1486tight positional0.480
22F1486tight positional0.660
11A1381tight thermal8.665
11B1381tight thermal7.630
11C1381tight thermal5.770
11D1381tight thermal8.980
11E1381tight thermal6.830
11F1381tight thermal19.470
22A1486tight thermal7.415
22B1486tight thermal10.50
22C1486tight thermal8.790
22D1486tight thermal21.020
22E1486tight thermal9.790
22F1486tight thermal32.070
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 261 -
Rwork0.321 8975 -
obs--92.61 %

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