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- PDB-2w8d: Distinct and essential morphogenic functions for wall- and lipo- ... -

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Basic information

Entry
Database: PDB / ID: 2w8d
TitleDistinct and essential morphogenic functions for wall- and lipo- teichoic acids in Bacillus subtilis
ComponentsPROCESSED GLYCEROL PHOSPHATE LIPOTEICHOIC ACID SYNTHASE 2
KeywordsTRANSFERASE / PHOSPHATASE / CELL MEMBRANE / TRANSMEMBRANE / LTA / WTA / MEMBRANE / SECRETED / CELL WALL / B.SUBTILIS / LIPOTECHOIC ACID / CELL WALL BIOGENESIS/DEGRADATION ACID
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / lipoteichoic acid biosynthetic process / cell wall organization / transferase activity / extracellular region / 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
DI(HYDROXYETHYL)ETHER / Lipoteichoic acid synthase 2
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsSchirner, K. / Marles-Wright, J. / Lewis, R.J. / Errington, J.
CitationJournal: Embo J. / Year: 2009
Title: Distinct and Essential Morphogenic Functions for Wall- and Lipo-Teichoic Acids in Bacillus Subtilis
Authors: Schirner, K. / Marles-Wright, J. / Lewis, R.J. / Errington, J.
History
DepositionJan 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: PROCESSED GLYCEROL PHOSPHATE LIPOTEICHOIC ACID SYNTHASE 2
B: PROCESSED GLYCEROL PHOSPHATE LIPOTEICHOIC ACID SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4656
Polymers101,1162
Non-polymers3494
Water4,197233
1
A: PROCESSED GLYCEROL PHOSPHATE LIPOTEICHOIC ACID SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8834
Polymers50,5581
Non-polymers3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROCESSED GLYCEROL PHOSPHATE LIPOTEICHOIC ACID SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5822
Polymers50,5581
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.627, 54.408, 140.783
Angle α, β, γ (deg.)90.00, 90.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROCESSED GLYCEROL PHOSPHATE LIPOTEICHOIC ACID SYNTHASE 2 / LTAS / LTA SYNTHASE 2 / POLYGLYCEROL PHOSPHATE SYNTHASE 2


Mass: 50557.852 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 214-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O34952, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8
Details: 150 MM MGCL2, 100 MM BICINE, PH 8.0 AND 25 % (W/V) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9699
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 2.35→70.36 Å / Num. obs: 704196 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 19.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.1
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.35→141.42 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.909 / SU B: 17.367 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1797 5 %RANDOM
Rwork0.17 ---
obs0.174 34148 99.9 %-
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: 21.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.7 Å2
2---1.6 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.35→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 0 22 233 7060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9549433
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4465839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74625.659364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.334151206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6871510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215400
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6081.54181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14926747
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18532812
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3334.52686
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
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 116 -
Rwork0.205 2463 -
obs--99.38 %
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)
11.8780.627-0.19164.36450.30691.30310.1363-0.09030.0730.6799-0.14370.47270.1930.02040.00740.2047-0.0340.17430.0966-0.03360.185837.738-5.64124.853
21.52930.6779-0.79473.9676-0.18963.43730.03740.43350.0728-0.67090.03040.4523-0.0917-0.4364-0.06770.25960.0096-0.10890.3637-0.01490.192238.849-0.22286.704
33.50112.1102-1.26128.1302-0.33443.50960.1163-0.00530.28190.32990.0883-0.8499-0.21670.4557-0.20460.07080.00940.02460.2108-0.0670.296859.2914.862122.61
43.1770.729-0.04276.5388-0.01117.6515-0.20110.0347-0.7983-0.4821-0.0398-0.98351.19720.62750.24090.34960.12320.12630.2884-0.04810.470256.85-16.02389.646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A216 - 550
2X-RAY DIFFRACTION1A594 - 635
3X-RAY DIFFRACTION2B215 - 550
4X-RAY DIFFRACTION2B594 - 635
5X-RAY DIFFRACTION3A551 - 593
6X-RAY DIFFRACTION4B551 - 593

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