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- PDB-4uop: Crystal structure of the lipoteichoic acid synthase LtaP from Lis... -

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Basic information

Entry
Database: PDB / ID: 4uop
TitleCrystal structure of the lipoteichoic acid synthase LtaP from Listeria monocytogenes
ComponentsLIPOTEICHOIC ACID PRIMASE
KeywordsTRANSFERASE / GRAM POSITIVE / CELL WALL
Function / homology
Function and homology information


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 ...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: 1.75 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOTEICHOIC ACID PRIMASE
B: LIPOTEICHOIC ACID PRIMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,22910
Polymers101,3602
Non-polymers8708
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-61.7 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.198, 53.700, 85.037
Angle α, β, γ (deg.)71.63, 76.78, 65.12
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 203 - 609 / Label seq-ID: 32 - 438

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.9998, 0.0094, 0.0163), (-0.0128, 0.2952, -0.9553), (-0.0138, -0.9554, -0.2951)
Vector: 112.1113, 35.8675, 77.5455)

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Components

#1: Protein LIPOTEICHOIC ACID PRIMASE / LMO0644 PROTEIN


Mass: 50679.809 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR CATALYTIC DOMAIN, RESIDUES 193-606
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: Q8Y989, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.08 Å3/Da / Density % sol: 40.86 % / Description: NONE
Crystal growpH: 5.4
Details: 100MM NA CACODYLATE PH 5.4, 100MM MGCL2, 33% PEG2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.75→47.96 Å / Num. obs: 77013 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W5Q

2w5q


Resolution: 1.75→80.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.973 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20738 3847 5 %RANDOM
Rwork0.17826 ---
obs0.17971 73165 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.899 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å2-0.42 Å21.15 Å2
2--2.1 Å2-0.69 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.75→80.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 34 481 7111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026796
X-RAY DIFFRACTIONr_bond_other_d0.0030.026168
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9569201
X-RAY DIFFRACTIONr_angle_other_deg0.8573.00114219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20525.419358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.325151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6091522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217829
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021601
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_it1.5872.9013270
X-RAY DIFFRACTIONr_mcbond_other1.5852.8993269
X-RAY DIFFRACTIONr_mcangle_it2.5344.3414085
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0713.2073526
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: 25928 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 279 -
Rwork0.296 5329 -
obs--92.72 %

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