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

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Basic information

Entry
Database: PDB / ID: 2wje
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
: / Tyrosine-protein phosphatase CpsB
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE CPSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6564
Polymers28,4911
Non-polymers1653
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.980, 58.540, 114.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.17 Å3/Da / Density % sol: 42.99 % / Description: NONE
Crystal growDetails: 0.1 M NA-ACETATE, 35% W/V PEG 400, PH 4.2

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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: 1.9→30 Å / Num. obs: 22224 / % possible obs: 92.5 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 14.86 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 64.4
Reflection shellHighest resolution: 1.9 Å / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 27.8 / % possible all: 61.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNRELEASED STRUCTURE

Resolution: 1.899→29.987 Å / SU ML: 0.48 / σ(F): 1.36 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 1158 5.2 %
Rwork0.1385 --
obs0.1412 22180 91.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.691 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0226 Å20 Å2-0 Å2
2--4.3513 Å2-0 Å2
3----0.3287 Å2
Refinement stepCycle: LAST / Resolution: 1.899→29.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 3 382 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092105
X-RAY DIFFRACTIONf_angle_d1.1062857
X-RAY DIFFRACTIONf_dihedral_angle_d14.815822
X-RAY DIFFRACTIONf_chiral_restr0.075313
X-RAY DIFFRACTIONf_plane_restr0.005367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8987-1.98510.172980.12451741X-RAY DIFFRACTION62
1.9851-2.08970.16261460.11412556X-RAY DIFFRACTION91
2.0897-2.22060.17071420.11822676X-RAY DIFFRACTION95
2.2206-2.3920.18361570.1242696X-RAY DIFFRACTION96
2.392-2.63260.18721570.13622733X-RAY DIFFRACTION96
2.6326-3.01320.18351450.13962790X-RAY DIFFRACTION97
3.0132-3.79520.20291650.14152821X-RAY DIFFRACTION98
3.7952-29.99030.20481480.15113009X-RAY DIFFRACTION99
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)
10.4872-0.03220.25290.49880.3080.3057-0.0039-0.17340.08230.0845-0.01360.0454-0.0301-0.08340.02790.0612-0.00620.0080.0734-0.03160.0566-11.886-3.315826.9328
20.2593-0.6426-0.19550.28720.52770.16880.1227-0.06080.2687-0.2173-0.0259-0.1121-0.2148-0.0704-0.07690.2330.097-0.00190.1536-0.10160.2804-25.00456.937415.7528
30.5577-0.0240.21940.0963-0.14060.54140.001-0.014-0.006-0.046-0.00280.02510.0471-0.02050.00340.074-0.008-0.00560.0520.00070.0585-16.7683-14.580411.7805
40.287-0.1447-0.33610.17750.09710.7604-0.0489-0.0182-0.0280.0944-0.04930.02230.0840.01580.07870.1135-0.0076-0.01810.0766-0.00430.1136-3.3349-18.063220.797
50.41810.0354-0.16270.80060.32760.3970.022-0.0309-0.0012-0.18070.0418-0.0452-0.07960.1229-0.06840.0702-0.0142-0.00070.07050.00270.072-2.233-8.53558.9686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:92)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 93:100)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 101:207)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 208:222)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 223:247)

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