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- PDB-1wra: Crystal Structure of Phosphorylcholine Esterase Domain of the Vir... -

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Basic information

Entry
Database: PDB / ID: 1wra
TitleCrystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E from Streptococcus Pneumoniae
ComponentsTeichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)
KeywordsHYDROLASE / phosphocholine / iron / esterase / choline / streptococcus / pneum / metallo / lactamase / PCE / CBPE
Function / homology
Function and homology information


ComA-like, MBL domain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase ...ComA-like, MBL domain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHOCHOLINE / Teichoic acid phosphorylcholine esterase/choline binding protein E (CbpE)
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsGarau, G. / Dideberg, O.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of phosphorylcholine esterase domain of the virulence factor choline-binding protein e from streptococcus pneumoniae: new structural features among the metallo-beta-lactamase superfamily
Authors: Garau, G. / Lemaire, D. / Vernet, T. / Dideberg, O. / Di Guilmi, A.M.
#1: Journal: MOL.MICROBIOL. / Year: 2001
Title: Identification of the teichoic acid phosphorylcholine esterase in Streptococcus pneumoniae
Authors: Vollmer, W. / Tomasz, A.
#2: Journal: NAT.STRUCT.BIOL. / Year: 2001
Title: A novel solenoid fold in the cell wall anchoring domain of the pneumococcal virulence factor LytA
Authors: Fernandez-Tornero, C. / Lopez, R. / Garzia, E. / Gimenez-Gallego, G. / Romero, A.
History
DepositionOct 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)
B: Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,14323
Polymers70,0912
Non-polymers2,05221
Water6,521362
1
A: Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,13112
Polymers35,0461
Non-polymers1,08511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,01311
Polymers35,0461
Non-polymers96710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)
hetero molecules

A: Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,26124
Polymers70,0912
Non-polymers2,17022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5980 Å2
ΔGint-212 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.302, 98.302, 172.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-544-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYAA30 - 3344 - 308
2GLUGLUBB27 - 3341 - 308

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)


Mass: 35045.672 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Species: Streptococcus pneumoniae / Strain: ATCC BAA-255 / R6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8DQ62, glycerophosphocholine cholinephosphodiesterase

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Non-polymers , 5 types, 383 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H15NO4P
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.37 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.54179 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2→23.84 Å / Num. all: 56344 / Num. obs: 56344 / % possible obs: 96.9 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 20 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 21.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.4 / % possible all: 96.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2→23.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.06 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.15 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2835 5.1 %RANDOM
Rwork0.174 ---
obs0.176 53117 96.73 %-
all-53117 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 30 451 5421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215161
X-RAY DIFFRACTIONr_bond_other_d0.0060.024506
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.9557008
X-RAY DIFFRACTIONr_angle_other_deg1.103310542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg25.3485617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1390.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025667
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021015
X-RAY DIFFRACTIONr_nbd_refined0.2130.2993
X-RAY DIFFRACTIONr_nbd_other0.2630.25207
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.22729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.220
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3350.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.53053
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67624942
X-RAY DIFFRACTIONr_scbond_it2.43232108
X-RAY DIFFRACTIONr_scangle_it3.9434.52049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1801medium positional0.170.5
2825loose positional0.375
1801medium thermal1.022
2825loose thermal1.6410
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 187
Rwork0.197 3480

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