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- PDB-2wjd: Crystal structure of the tyrosine phosphatase Cps4B from Steptoco... -

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Basic information

Entry
Database: PDB / ID: 2wjd
TitleCrystal structure of the tyrosine phosphatase Cps4B from Steptococcus pneumoniae TIGR4.
ComponentsTYROSINE-PROTEIN PHOSPHATASE CPSB
KeywordsHYDROLASE / CAPSULE BIOGENESIS/DEGRADATION / MANGANESE / PHOSPHATASE / PROTEIN PHOSPHATASE / EXOPOLYSACCHARIDE SYNTHESIS
Function / homology
Function and homology information


capsule polysaccharide biosynthetic process / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / manganese ion binding
Similarity search - Function
: / Capsular polysaccharide synthesis, CpsB/CapC / Capsular polysaccharide synthesis, CpsB/CapC / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / SAMARIUM (III) ION / Tyrosine-protein phosphatase CpsB
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.799 Å
AuthorsHagelueken, G. / Huang, H. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of Wzb of Escherichia Coli and Cpsb of Streptococcus Pneumoniae, Representatives of Two Families of Tyrosine Phosphatases that Regulate Capsule Assembly.
Authors: Hagelueken, G. / Huang, H. / Mainprize, I.L. / Whitfield, C. / Naismith, J.H.
History
DepositionMay 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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: TYROSINE-PROTEIN PHOSPHATASE CPSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,43711
Polymers28,4911
Non-polymers94610
Water1,31573
1
A: TYROSINE-PROTEIN PHOSPHATASE CPSB
hetero molecules

A: TYROSINE-PROTEIN PHOSPHATASE CPSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,87322
Polymers56,9812
Non-polymers1,89220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4400 Å2
ΔGint-166.19 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.850, 88.850, 92.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2069-

HOH

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE CPSB / CPS4B


Mass: 28490.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR 4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9AHD4, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sm
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.21 Å3/Da / Density % sol: 61.53 % / Description: NONE
Crystal growDetails: 2 M (NH4)2SO4, 0.1 M TRIS-CL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 9531 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 22.4 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 58.9
Reflection shellHighest resolution: 2.8 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 18.2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.799→29.076 Å / SU ML: 2.01 / σ(F): 2.21 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 458 4.8 %
Rwork0.1731 --
obs0.176 9507 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.437 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0676 Å20 Å20 Å2
2---0.0676 Å20 Å2
3---0.1352 Å2
Refinement stepCycle: LAST / Resolution: 2.799→29.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 30 73 2084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062039
X-RAY DIFFRACTIONf_angle_d0.9312751
X-RAY DIFFRACTIONf_dihedral_angle_d16.605769
X-RAY DIFFRACTIONf_chiral_restr0.065300
X-RAY DIFFRACTIONf_plane_restr0.003352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7991-3.20370.30631430.20622943X-RAY DIFFRACTION100
3.2037-4.03460.2431520.16012958X-RAY DIFFRACTION99
4.0346-29.07730.18691630.15923148X-RAY DIFFRACTION100
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)
10.9276-0.16560.00661.15350.63871.03550.08690.1031-0.0392-0.1594-0.0195-0.0777-0.2622-0.0524-0.07120.16090.0190.00020.1098-0.00480.128371.507252.638436.7425
22.25361.1696-1.5825-3.3044-1.54915.8943-0.1977-0.1093-0.5819-0.1689-0.1265-0.17240.51120.22390.30510.246-0.0030.0080.01180.04030.215277.352936.603348.8224
30.7698-0.0148-0.00470.33480.33380.6182-0.0944-0.0526-0.17860.11670.06240.01460.1761-0.08360.05690.1073-0.00620.04260.0554-0.01950.12365.223239.019944.4483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:138)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 139:155)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 156:247)

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