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- PDB-4uoo: Structure of lipoteichoic acid synthase LtaS from Listeria monocy... -

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Basic information

Entry
Database: PDB / ID: 4uoo
TitleStructure of lipoteichoic acid synthase LtaS from Listeria monocytogenes
ComponentsLIPOTEICHOIC ACID SYNTHASE
KeywordsTRANSFERASE / LIPOTEICHOIC ACID SYNTHESIS / CELL WALL / GRAM POSITIVE
Function / homology
Function and homology information


transferase activity / metal ion binding / membrane / plasma membrane
Similarity search - Function
Arylsulfatase, C-terminal domain - #170 / Lipoteichoic acid synthase-like / : / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 2-Layer Sandwich ...Arylsulfatase, C-terminal domain - #170 / Lipoteichoic acid synthase-like / : / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCampeotto, I. / Freemont, P. / Grundling, A.
CitationJournal: J. Biol. Chem. / Year: 2014
Title: Structural and mechanistic insight into the Listeria monocytogenes two-enzyme lipoteichoic acid synthesis system.
Authors: Campeotto, I. / Percy, M.G. / MacDonald, J.T. / Forster, A. / Freemont, P.S. / Grundling, A.
History
DepositionJun 6, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Other
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOTEICHOIC ACID SYNTHASE
B: LIPOTEICHOIC ACID SYNTHASE
C: LIPOTEICHOIC ACID SYNTHASE
D: LIPOTEICHOIC ACID SYNTHASE
E: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,39010
Polymers262,2685
Non-polymers1225
Water00
1
A: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4782
Polymers52,4541
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4782
Polymers52,4541
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4782
Polymers52,4541
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4782
Polymers52,4541
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4782
Polymers52,4541
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.760, 119.760, 473.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 230 - 644 / Label seq-ID: 36 - 450

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.8607, 0.509, 0.0128), (-0.509, -0.8608, 0.0056), (0.0139, -0.0017, 0.9999)-90.3406, 51.7635, -39.0678
3given(0.8781, 0.4784, -0.0024), (0.4784, -0.8781, -0.0029), (-0.0035, 0.0014, -1)-5.7969, 149.8961, 79.0367
4given(0.5031, -0.8641, -0.0155), (0.8642, 0.5031, 0.0083), (0.0007, -0.0176, 0.9998)32.1268, 111.1295, -78.2585
5given(-0.5151, -0.8571, -0.0065), (-0.8569, 0.5148, 0.025), (-0.018, 0.0185, -0.9997)-67.9831, 28.9146, 38.8665
6given(1), (1), (1)
7given(-0.514628, -0.857401, -0.004655), (-0.857164, 0.51434, 0.026905), (-0.020674, 0.017836, -0.999627)-68.01523, 28.81536, 38.74216
8given(0.502595, -0.864356, -0.016952), (0.864521, 0.502522, 0.008658), (0.001036, -0.019007, 0.999819)32.22073, 111.13499, -78.15736
9given(0.878512, 0.477721, -0.000283), (0.477715, -0.878505, -0.004218), (-0.002263, 0.003571, -0.999991)-5.87117, 149.96748, 78.94776
10given(-0.860344, 0.509584, 0.011492), (-0.509547, -0.860421, 0.006176), (0.013035, -0.000542, 0.999915)-90.27109, 51.69691, -39.13647

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Components

#1: Protein
LIPOTEICHOIC ACID SYNTHASE / LMO0927 PROTEIN


Mass: 52453.633 Da / Num. of mol.: 5 / Fragment: EXTRACELLULAR CATALYTIC DOMAIN, RESIDUES 226-653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q8Y8H6, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 65.28 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.64M NA ACETATE PH 4.6, 4% PEG3350, 100 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→106.88 Å / Num. obs: 63877 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W8D

2w8d


Resolution: 3→108.88 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25996 3201 5 %RANDOM
Rwork0.22215 ---
obs0.22405 60591 90.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2--1.17 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 3→108.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16740 0 5 0 16745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0217170
X-RAY DIFFRACTIONr_bond_other_d00.0215510
X-RAY DIFFRACTIONr_angle_refined_deg0.791.95323245
X-RAY DIFFRACTIONr_angle_other_deg3.575335875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.28552070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05525.562890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98152860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4851525
X-RAY DIFFRACTIONr_chiral_restr0.030.22415
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02119825
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024110
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1764.9588295
X-RAY DIFFRACTIONr_mcbond_other5.1744.9588294
X-RAY DIFFRACTIONr_mcangle_it7.2527.42510360
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.7015.0938875
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6450 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A8.34
2B11.56
3C6.65
4D11.34
5E7.47
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 212 -
Rwork0.319 4057 -
obs--83.3 %

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