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

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Basic information

Entry
Database: PDB / ID: 2wmy
TitleCrystal structure of the tyrosine phosphatase Wzb from Escherichia coli K30 in complex with sulphate.
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 / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.211 Å
AuthorsHuang, H. / Hagelueken, G. / Whitfield, C. / Naismith, J.H.
CitationJournal: To be Published
Title: Crystal Structures of the Capsular Export Regulating Tyrosine Phosphatases Wzb of Escherichia Coli and Cpsb of Streptococcus Pneumoniae.
Authors: Hagelueken, G. / Huang, H. / Mainprize, I.L. / Whitfield, C. / Naismith, J.H.
History
DepositionJul 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 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.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
C: PUTATIVE ACID PHOSPHATASE WZB
D: PUTATIVE ACID PHOSPHATASE WZB
E: PUTATIVE ACID PHOSPHATASE WZB
F: PUTATIVE ACID PHOSPHATASE WZB
G: PUTATIVE ACID PHOSPHATASE WZB
H: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,57822
Polymers134,3078
Non-polymers1,27014
Water10,665592
1
A: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9433
Polymers16,7881
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0394
Polymers16,7881
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8842
Polymers16,7881
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8842
Polymers16,7881
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8842
Polymers16,7881
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9813
Polymers16,7881
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8842
Polymers16,7881
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: PUTATIVE ACID PHOSPHATASE WZB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0774
Polymers16,7881
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.902, 53.062, 113.909
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PUTATIVE ACID PHOSPHATASE WZB / WZB


Mass: 16788.420 Da / Num. of mol.: 8 / Mutation: YES
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, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 48 TO THR ENGINEERED RESIDUE IN CHAIN B, ALA 48 TO THR ...ENGINEERED RESIDUE IN CHAIN A, ALA 48 TO THR ENGINEERED RESIDUE IN CHAIN B, ALA 48 TO THR ENGINEERED RESIDUE IN CHAIN C, ALA 48 TO THR ENGINEERED RESIDUE IN CHAIN D, ALA 48 TO THR ENGINEERED RESIDUE IN CHAIN E, ALA 48 TO THR ENGINEERED RESIDUE IN CHAIN F, ALA 48 TO THR ENGINEERED RESIDUE IN CHAIN G, ALA 48 TO THR ENGINEERED RESIDUE IN CHAIN H, ALA 48 TO THR

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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: 2.26 Å3/Da / Density % sol: 45.7 % / Description: NONE
Crystal growDetails: 0.1M TRIS-CL PH 8.5, 1.2 M LI2SO4, 0.01M NICL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDate: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→34 Å / Num. obs: 59360 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27.97 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.1
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 80.8

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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: PDB ENTRY 2WJA

2wja


Resolution: 2.211→33.967 Å / SU ML: 0.77 / σ(F): 1.33 / Phase error: 28.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2606 2987 5 %
Rwork0.2063 --
obs0.2091 59360 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.41 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4497 Å20 Å20.2166 Å2
2--6.3795 Å2-0 Å2
3----4.9299 Å2
Refinement stepCycle: LAST / Resolution: 2.211→33.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9021 0 62 592 9675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059275
X-RAY DIFFRACTIONf_angle_d0.88412497
X-RAY DIFFRACTIONf_dihedral_angle_d16.3533493
X-RAY DIFFRACTIONf_chiral_restr0.0641384
X-RAY DIFFRACTIONf_plane_restr0.0031585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2107-2.2470.26191050.22462149X-RAY DIFFRACTION78
2.247-2.28570.32941240.22792519X-RAY DIFFRACTION91
2.2857-2.32730.32891380.24272632X-RAY DIFFRACTION95
2.3273-2.3720.32851330.24462656X-RAY DIFFRACTION96
2.372-2.42040.31561210.24212721X-RAY DIFFRACTION97
2.4204-2.4730.33481430.23252637X-RAY DIFFRACTION97
2.473-2.53050.31791430.21212704X-RAY DIFFRACTION97
2.5305-2.59380.32241410.22112667X-RAY DIFFRACTION97
2.5938-2.66390.28921360.23332728X-RAY DIFFRACTION98
2.6639-2.74230.32191630.23382668X-RAY DIFFRACTION97
2.7423-2.83070.2811380.23532714X-RAY DIFFRACTION97
2.8307-2.93180.31091670.23762666X-RAY DIFFRACTION98
2.9318-3.04920.25271300.21872720X-RAY DIFFRACTION97
3.0492-3.18780.27311590.21092736X-RAY DIFFRACTION99
3.1878-3.35580.2641580.19872703X-RAY DIFFRACTION99
3.3558-3.56580.2111420.16862791X-RAY DIFFRACTION99
3.5658-3.84080.19961440.15452757X-RAY DIFFRACTION99
3.8408-4.22660.18381530.14162771X-RAY DIFFRACTION99
4.2266-4.83680.19861470.14812803X-RAY DIFFRACTION99
4.8368-6.08810.21391500.1692799X-RAY DIFFRACTION99
6.0881-33.97130.23861520.19682832X-RAY DIFFRACTION97
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)
12.5434-1.1832-0.560.79960.54592.2304-0.0413-0.10970.13680.02230.0657-0.0571-0.00510.0857-0.01350.1073-0.0139-0.01270.0868-0.00180.116910.54869.2354-18.239
22.285-0.4635-0.77110.81550.29742.2081-0.00860.1809-0.03570.0902-0.0433-0.05390.132-0.12610.04190.0679-0.012-0.01130.07590.01190.0974-15.737711.8278-38.7662
31.9460.96820.99031.80841.15082.70650.0952-0.055-0.07340.1088-0.0682-0.1813-0.1022-0.1261-0.02660.10750.0041-0.04260.06490.00830.1318-11.8247-15.1886-17.3761
41.99090.32291.16951.45430.91372.2284-0.00280.3735-0.2629-0.0054-0.00490.00110.05510.08270.00010.11890.0131-0.00950.2275-0.07590.1614.3601-13.6941-39.5551
52.3613-1.06650.73081.3795-0.8152.5454-0.0265-0.0436-0.09450.04390.060.0446-0.0004-0.0838-0.03740.098-0.00580.01190.06930.00070.1097-61.462-9.3466-18.2103
62.0917-0.62440.99740.5670.00161.66280.02690.19760.01140.0172-0.09060.0456-0.15040.13770.05660.089-0.02440.0120.1103-0.00160.1027-35.2612-11.8592-38.7969
72.22370.7501-0.7231.6103-1.23582.94020.0913-0.02860.05750.1278-0.0540.15580.06520.1533-0.01330.1081-0.0060.03610.0515-0.00830.114-39.041815.1025-17.5525
81.87660.3862-1.15151.7378-1.0842.0729-0.0080.35890.2205-0.0342-0.0068-0.01780.0131-0.1010.03310.0720.00270.01610.19060.06940.1339-65.335413.4928-39.4099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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