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

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Basic information

Entry
Database: PDB / ID: 4uor
TitleStructure of lipoteichoic acid synthase LtaS from Listeria monocytogenes in complex with glycerol phosphate
ComponentsLIPOTEICHOIC ACID SYNTHASE
KeywordsTRANSFERASE / LIPOTEICHOIC ACID SYNTHESIS / CELL WALL / LTAS / GRAM POSITIVE
Function / homology
Function and homology information


sulfuric ester hydrolase activity / metal ion binding / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl phosphate / Lmo0927 protein
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES EGD-E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 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 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Structure summary
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_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_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

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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
F: LIPOTEICHOIC ACID SYNTHASE
G: LIPOTEICHOIC ACID SYNTHASE
H: LIPOTEICHOIC ACID SYNTHASE
I: LIPOTEICHOIC ACID SYNTHASE
J: LIPOTEICHOIC ACID SYNTHASE
K: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)579,12833
Polymers576,99011
Non-polymers2,13822
Water53,9912997
1
A: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: LIPOTEICHOIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6483
Polymers52,4541
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.246, 119.625, 472.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9994, -0.0308, -0.0143), (-0.0314, 0.9987, 0.0403), (0.0131, 0.0407, -0.9991)-61.0785, 47.4423, -236.3995
3given(-0.5016, 0.8648, -0.0209), (0.8649, 0.5019, 0.0094), (0.0186, -0.0134, -0.9997)-14.6116, 76.5447, -157.8062
4given(0.8942, -0.4391, -0.087), (-0.4415, -0.8972, -0.0101), (-0.0736, 0.0474, -0.9962)-37.5205, -6.2993, -193.0551
5given(0.8682, -0.4893, -0.082), (-0.4866, -0.8721, 0.0521), (-0.097, -0.0053, -0.9953)19.3357, -13.8183, -202.7679
6given(-0.8463, 0.5229, 0.1018), (-0.5278, -0.8489, -0.0279), (0.0718, -0.0774, 0.9944)-16.0025, 38.2056, -38.0822
7given(0.0109, -0.9964, -0.0835), (-0.9994, -0.0137, 0.0325), (-0.0335, 0.0831, -0.996)-28.9028, -24.4397, -118.5679
8given(0.4916, -0.8706, 0.0168), (0.8702, 0.4905, -0.0467), (0.0324, 0.0376, 0.9988)13.9777, 14.7882, -80.3287
9given(0.0563, 0.9968, 0.057), (-0.9975, 0.0585, -0.0384), (-0.0416, -0.0547, 0.9976)-28.1606, 19.9534, -118.6142
10given(0.4788, -0.8777, 0.0202), (0.8779, 0.4789, -0.0007), (-0.009, 0.0181, 0.9998)-44.0658, 30.9776, -78.1212
11given(-0.5925, 0.8047, -0.0383), (0.8055, 0.5922, -0.0207), (0.0061, -0.0431, -0.9991)-77.9197, 50.1569, -157.5004

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Components

#1: Protein
LIPOTEICHOIC ACID SYNTHASE / LMO0927 PROTEIN


Mass: 52453.633 Da / Num. of mol.: 11 / Fragment: EXTRACELLULAR CATALYTIC DOMAIN, RESIDUES 225-653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES EGD-E (bacteria)
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.: 11 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GP9 / (2R)-2,3-dihydroxypropyl phosphate / Glycerol 3-phosphate


Mass: 170.058 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2997 / 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: 3.1 Å3/Da / Density % sol: 60.7 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.64M NA ACETATE PH 4.6, 4% PEG3350, 100MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twinOperator: K,H,-L / Fraction: 0
ReflectionResolution: 2.2→48.71 Å / Num. obs: 335456 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UOO

4uoo


Resolution: 2.194→48.71 Å / σ(F): 0 / Phase error: 19.81 / Stereochemistry target values: TWIN_LSQ_F
Details: PHE K 282 AND LYSK 459 ARE C-BETA OUTLIERS. NO DENSITY FOR THESE RESIDUES. TPO307 WAS EXCLUDED FROM NCS IN EACH MONOMER BY PHENIX REFINEMENT WITH REFMAC DETECTS 9 PERCENT TWINNING WITH ...Details: PHE K 282 AND LYSK 459 ARE C-BETA OUTLIERS. NO DENSITY FOR THESE RESIDUES. TPO307 WAS EXCLUDED FROM NCS IN EACH MONOMER BY PHENIX REFINEMENT WITH REFMAC DETECTS 9 PERCENT TWINNING WITH OPERATOR K,H,-L. FINAL REFINEMENT IN PHENIX DOES NOT DETECT ANY TWINNING. THIS DISCREPANCY IS PROBABLY DUE TO THE DISORDER OF MONOMER K.
RfactorNum. reflection% reflection
Rfree0.2136 17158 5 %
Rwork0.1782 --
obs0.1799 335456 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37000 0 121 2997 40118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00738189
X-RAY DIFFRACTIONf_angle_d1.0751732
X-RAY DIFFRACTIONf_dihedral_angle_d14.17113966
X-RAY DIFFRACTIONf_chiral_restr0.0455370
X-RAY DIFFRACTIONf_plane_restr0.0066776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1945-2.23240.23667590.208314061X-RAY DIFFRACTION82
2.2324-2.2730.21878520.195516194X-RAY DIFFRACTION95
2.273-2.31670.20988340.194216263X-RAY DIFFRACTION95
2.3167-2.3640.22148910.191616139X-RAY DIFFRACTION95
2.364-2.41540.21218490.192616220X-RAY DIFFRACTION95
2.4154-2.47150.22949060.198516177X-RAY DIFFRACTION95
2.4715-2.53330.20818540.192116257X-RAY DIFFRACTION95
2.5333-2.60180.2168480.186516257X-RAY DIFFRACTION95
2.6018-2.67840.23468560.194216226X-RAY DIFFRACTION95
2.6784-2.76480.23739010.197516138X-RAY DIFFRACTION94
2.7648-2.86360.24338980.197616288X-RAY DIFFRACTION95
2.8636-2.97830.24138630.194516268X-RAY DIFFRACTION95
2.9783-3.11380.26298190.198616317X-RAY DIFFRACTION95
3.1138-3.27790.23128400.188416351X-RAY DIFFRACTION95
3.2779-3.48330.23488780.181616372X-RAY DIFFRACTION95
3.4833-3.75210.2118000.167516495X-RAY DIFFRACTION95
3.7521-4.12950.18638500.14616347X-RAY DIFFRACTION95
4.1295-4.72660.17518550.139716519X-RAY DIFFRACTION95
4.7266-5.95330.18749010.162416634X-RAY DIFFRACTION95
5.9533-48.42330.21379040.188617044X-RAY DIFFRACTION94

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