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- PDB-2wja: Crystal structure of the tyrosine phosphatase Wzb from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 2wja
TitleCrystal structure of the tyrosine phosphatase Wzb from Escherichia coli K30 in complex with phosphate.
ComponentsPUTATIVE ACID PHOSPHATASE WZB
KeywordsHYDROLASE / PHOSPHATASE
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
: / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, H. / Hagelueken, G. / Whitfield, C. / 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 1.3Dec 13, 2023Group: 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.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_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: PUTATIVE ACID PHOSPHATASE WZB
B: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8525
Polymers37,6032
Non-polymers2493
Water34219
1
A: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9553
Polymers18,8021
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8972
Polymers18,8021
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.030, 90.030, 83.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1149-

NI

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Components

#1: Protein PUTATIVE ACID PHOSPHATASE WZB


Mass: 18801.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9X4B8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.94 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growDetails: 0.2 M K2HPO4, 18% W/V PEG 3350, 0.1 M TRIS-CL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 12623 / % possible obs: 90.8 % / Observed criterion σ(I): 3 / Redundancy: 8.7 % / Biso Wilson estimate: 65.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.3
Reflection shellHighest resolution: 2.5 Å / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FEK

2fek


Resolution: 2.5→28.5 Å / SU ML: 0.13 / σ(F): 1.38 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 636 5.1 %
Rwork0.2198 --
obs0.2224 12601 90.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.971 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.1165 Å2-0 Å2-0 Å2
2--9.1165 Å2-0 Å2
3----18.2329 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 11 19 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022267
X-RAY DIFFRACTIONf_angle_d0.573046
X-RAY DIFFRACTIONf_dihedral_angle_d12.358848
X-RAY DIFFRACTIONf_chiral_restr0.041338
X-RAY DIFFRACTIONf_plane_restr0.002384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.69320.3691230.30232090X-RAY DIFFRACTION82
2.6932-2.9640.32171400.24312603X-RAY DIFFRACTION100
2.964-3.39220.32261490.22582603X-RAY DIFFRACTION100
3.3922-4.27160.267880.19811967X-RAY DIFFRACTION74
4.2716-28.50180.23031360.20832702X-RAY DIFFRACTION98
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)
16.44350.6195-0.20342.5554-1.91142.3592-0.0909-0.25530.19911.0470.1188-0.3923-0.4255-0.26040.10040.32230.06770.10560.46220.11530.21321.6776-32.6886-3.741
28.85072.1847-5.75523.19050.2749-1.4199-0.4348-0.05510.47620.370.39390.1285-0.1438-0.0737-0.06930.487-0.01350.11660.6590.06210.49.7585-33.4853-8.5542
3-3.48646.32073.17373.2782-0.68623.87390.33771.4654-1.1969-0.97371.27510.20041.92640.2525-0.63040.327-0.11590.15840.6456-0.1190.26070.9002-41.9419-6.159
46.6035-0.48612.0225-3.7795-0.85147.4205-0.4754-1.1736-3.45321.30411.4081.62142.3676-0.7762-0.54181.1916-0.05380.32450.75960.49391.65194.7112-48.7424-0.8096
52.5288-2.82051.87731.3455-4.44544.0675-1.17510.3453-0.19870.01930.90270.29081.0986-2.66541.10210.6918-0.28240.4860.92040.28370.9378-4.5011-41.5314-2.1536
63.4455-1.7782-0.30023.5430.6852.88140.112.6958-1.078-0.4995-0.90350.68830.0981-1.52520.69720.2277-0.11620.08311.4042-0.07020.4589-1.5366-37.4836-17.0818
72.0751-0.25260.8212-1.14270.00646.8753-0.41240.0737-0.0281-0.1245-0.07890.1389-0.66740.19020.35460.39480.0377-0.04450.4985-0.05950.3652-18.7645-25.0079-27.3017
8-1.71461.696-1.79056.1922-6.81596.5483-0.93620.16950.0091-0.70021.97060.5648-1.6942-4.87-0.62310.72350.6264-0.11921.25910.09190.3586-24.5287-24.0338-41.5059
90.0564-0.3106-1.29975.48553.57648.86620.12990.0589-0.267-0.16610.24640.3035-0.13430.3112-0.20850.3557-0.0143-0.10510.7578-0.1350.4824-18.5927-29.9512-26.4143
102.29419.04490.5796.27626.17588.73131.5138-2.8424-0.14082.3299-0.70081.39944.6257-0.2486-0.23130.98730.10110.13441.4101-0.1080.5898-27.9102-36.2243-18.6524
110.9105-1.6831-1.44923.2361-1.048-1.72320.1139-0.7593-0.06630.6849-0.57370.6164-0.5639-0.47170.26010.66880.26920.03261.1088-0.34120.4824-29.4598-22.718-19.2989
123.20921.1156-0.9841.1321.35673.4157-0.23940.18620.7822-0.588-0.26651.5283-1.3303-0.37590.55130.94110.5751-0.42060.5752-0.3660.8808-29.7976-18.0953-31.4391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -3:45)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 46:82)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 83:87)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 88:101)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 102:112)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 113:143)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 2:46)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 47:61)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 62:87)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 88:101)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 102:119)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 120:143)

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