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- PDB-4az1: Crystal structure of the Trypanosoma cruzi protein tyrosine phosp... -

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Basic information

Entry
Database: PDB / ID: 4az1
TitleCrystal structure of the Trypanosoma cruzi protein tyrosine phosphatase TcPTP1, a potential therapeutic target for Chagas' disease
ComponentsTYROSINE SPECIFIC PROTEIN PHOSPHATASE
KeywordsHYDROLASE / DRUG DESIGN
Function / homology
Function and homology information


protein tyrosine phosphatase activity
Similarity search - Function
Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site ...Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Tyrosine specific protein phosphatase, putative
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.181 Å
AuthorsLountos, G.T. / Tropea, J.E. / Waugh, D.S.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2012
Title: Structure of the Trypanosoma Cruzi Protein Tyrosine Phosphatase Tcptp1, a Potential Therapeutic Target for Chagas' Disease.
Authors: Lountos, G.T. / Tropea, J.E. / Waugh, D.S.
History
DepositionJun 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Dec 20, 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 / 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 / _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: TYROSINE SPECIFIC PROTEIN PHOSPHATASE
B: TYROSINE SPECIFIC PROTEIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9648
Polymers67,6712
Non-polymers2926
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint0.1 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.285, 154.285, 195.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein TYROSINE SPECIFIC PROTEIN PHOSPHATASE / PROTEIN TYROSINE PHOSPHATASE TCPTP1


Mass: 33835.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PJT206 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4E4C8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 3.32 Å3/Da / Density % sol: 62.9 % / Description: NONE
Crystal growDetails: 3.2 M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 46460 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 43.38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 37
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M4U

3m4u


Resolution: 2.181→30.941 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 2011 4.3 %
Rwork0.1896 --
obs0.1914 46377 99.34 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.18 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0917 Å20 Å20 Å2
2--0.0917 Å20 Å2
3----0.1834 Å2
Refinement stepCycle: LAST / Resolution: 2.181→30.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 19 261 4837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084686
X-RAY DIFFRACTIONf_angle_d1.0596365
X-RAY DIFFRACTIONf_dihedral_angle_d13.4521715
X-RAY DIFFRACTIONf_chiral_restr0.069732
X-RAY DIFFRACTIONf_plane_restr0.005818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1814-2.2360.34441470.28693084X-RAY DIFFRACTION98
2.236-2.29640.29321430.25193141X-RAY DIFFRACTION99
2.2964-2.3640.27611400.23613144X-RAY DIFFRACTION100
2.364-2.44020.29211440.23233161X-RAY DIFFRACTION100
2.4402-2.52740.26641430.22163158X-RAY DIFFRACTION100
2.5274-2.62860.28051350.22653194X-RAY DIFFRACTION100
2.6286-2.74810.28631480.21883153X-RAY DIFFRACTION100
2.7481-2.89290.28391370.22523156X-RAY DIFFRACTION100
2.8929-3.0740.30441440.22083191X-RAY DIFFRACTION100
3.074-3.31110.23381450.20653172X-RAY DIFFRACTION100
3.3111-3.64380.2321420.18563194X-RAY DIFFRACTION100
3.6438-4.170.20361480.16353187X-RAY DIFFRACTION100
4.17-5.24960.16491470.13393220X-RAY DIFFRACTION99
5.2496-30.94410.21041480.18433211X-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)
13.65471.1692-1.7692.1666-0.11332.22830.28030.07880.90250.2938-0.09040.4764-0.3121-0.1997-0.13820.3016-0.00950.03160.195-0.02270.49522.4188-47.397516.9644
24.31580.9101-0.2741.8040.27762.4654-0.14780.06690.35040.08060.10150.40920.1761-0.3322-0.01770.2672-0.0564-0.02090.211-0.0080.3089-9.1214-62.69415.9959
36.22520.99050.70693.2097-0.02512.226-0.20450.75090.0611-0.38680.18530.19490.2307-0.19380.00720.3718-0.1163-0.00310.29380.02420.204-4.7432-64.83457.5478
43.97091.3396-1.95922.7349-0.91765.3404-0.13790.52080.5827-0.2450.18210.05540.1058-0.035-0.02910.2458-0.0684-0.02480.22290.06570.32569.2055-50.61596.3439
52.9693-0.816-0.01770.3123-0.42482.0888-0.2458-0.44720.99780.4490.18370.4643-0.4249-0.6946-0.38850.66480.16710.3150.4748-0.23960.9979-30.7756-51.686641.525
63.94941.31020.77787.42711.16144.5042-0.0804-0.3457-0.14550.45440.3242-0.3703-0.09380.4706-0.19460.22010.00180.08450.3867-0.08730.2799-11.3248-75.314836.3068
72.20071.0253-0.25722.82140.5253.816-0.1165-0.2010.2750.41910.16510.4826-0.0978-0.12160.00970.28530.00710.13890.3259-0.00790.3213-23.998-80.184136.8045
83.7442-0.4933-0.54237.4579-0.34594.9979-0.08830.3999-0.1719-0.13660.00560.33750.7754-0.2854-0.00210.2536-0.01310.08960.39690.00620.3449-27.3514-92.34328.829
94.6192-1.6195-1.3962.32231.2122.84130.0097-0.12650.46720.26740.17630.58940.0392-0.4424-0.05410.188-0.01980.22860.44120.01670.5976-34.616-83.950936.9845
100.42190.30990.15341.1747-0.31570.25690.159-0.56880.54050.71630.13470.7824-0.2904-0.00760.23920.52830.01540.45680.4426-0.16710.5735-27.8378-67.93944.6774
116.9081-0.76690.39712.4312-0.6494.9758-0.2601-0.2861.38840.18760.45990.9243-0.4687-0.9917-0.21790.44090.03540.14550.4705-0.01980.9407-33.3175-60.15937.7766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:77)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 78:155)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 156:231)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 232:300)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 4:30)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 31:78)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 79:128)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 129:150)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 151:215)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 216:266)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 267:295)

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