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- PDB-9mex: Structure of phosphocysteine intermediate of human PRL1 phosphatase -

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Basic information

Entry
Database: PDB / ID: 9mex
TitleStructure of phosphocysteine intermediate of human PRL1 phosphatase
ComponentsProtein tyrosine phosphatase type IVA 1
KeywordsHYDROLASE / Phosphatase fold / alpha and beta protein / phosphocysteine
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / spindle / cytoplasmic side of plasma membrane / early endosome / positive regulation of cell migration / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
: / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Protein tyrosine phosphatase type IVA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMahbub, L. / Kozlov, G. / Knorn, C. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-07195 Canada
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structure of the phosphocysteine intermediate of the phosphatase of regenerating liver PTP4A1.
Authors: Mahbub, L. / Kozlov, G. / Knorn, C. / Gehring, K.
History
DepositionDec 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 25, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine phosphatase type IVA 1
B: Protein tyrosine phosphatase type IVA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1227
Polymers37,6412
Non-polymers4805
Water21612
1
A: Protein tyrosine phosphatase type IVA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1094
Polymers18,8211
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein tyrosine phosphatase type IVA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0133
Polymers18,8211
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.164, 148.164, 148.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 9 through 34 or (resid 35...
d_2ens_1(chain "B" and (resid 9 through 26 or resid 28...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROPHEPHEAA9 - 16013 - 164
d_21PROPROTHRTHRBB9 - 2613 - 30
d_22ALAALAPHEPHEBB28 - 16032 - 164

NCS oper: (Code: givenMatrix: (0.366668480211, 0.885582916496, -0.285126504608), (0.89379080563, -0.250237507145, 0.372181656976), (0.258248371517, -0.391310730786, -0.883280074823)Vector: 47. ...NCS oper: (Code: given
Matrix: (0.366668480211, 0.885582916496, -0.285126504608), (0.89379080563, -0.250237507145, 0.372181656976), (0.258248371517, -0.391310730786, -0.883280074823)
Vector: 47.2438027987, -25.8540659716, -47.9386464421)

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Components

#1: Protein Protein tyrosine phosphatase type IVA 1 / PTP(CAAXI) / Protein-tyrosine phosphatase 4a1 / Protein-tyrosine phosphatase of regenerating liver 1 / PRL-1


Mass: 18820.727 Da / Num. of mol.: 2 / Fragment: residues 7-160 / Mutation: C49S, D72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP4A1, PRL1, PTPCAAX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93096, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium nitrate and 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16735 / % possible obs: 100 % / Redundancy: 20.8 % / Biso Wilson estimate: 78.11 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.104 / Net I/σ(I): 94.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 20.3 % / Rmerge(I) obs: 2.338 / Num. unique obs: 1659 / CC1/2: 0.671 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19_4092phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.85 Å / SU ML: 0.4555 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.5422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 867 5.18 %
Rwork0.1937 15868 -
obs0.1959 16735 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.81 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 25 12 2382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482418
X-RAY DIFFRACTIONf_angle_d0.80213298
X-RAY DIFFRACTIONf_chiral_restr0.0484378
X-RAY DIFFRACTIONf_plane_restr0.0058413
X-RAY DIFFRACTIONf_dihedral_angle_d5.6686331
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.0622319697 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.770.34241330.30022626X-RAY DIFFRACTION100
2.77-2.980.38341430.2972624X-RAY DIFFRACTION100
2.98-3.280.3181530.28262609X-RAY DIFFRACTION100
3.28-3.750.23781810.2232587X-RAY DIFFRACTION100
3.76-4.730.19561310.16872671X-RAY DIFFRACTION100
4.73-46.850.21371260.15632751X-RAY DIFFRACTION99.93
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)
12.72493521216-3.26579538814-1.32988790624.56693942639-0.1052173739544.77447134503-0.195875263714-0.3953247474770.5373179451520.3921102389810.335546158195-0.770552371037-0.2648648201160.676761461781-0.09964556856520.500513941927-0.071060246696-0.08348131126640.606912624008-0.03535891664710.7253952951671.5513532744-20.6248642504-9.19666305622
23.18679851133-1.59221825751-1.239667425624.12856165783-1.575043467597.83536473061-0.0244691667203-0.2473458380780.0832871657542-0.155249167993-0.0487218186024-0.587418168470.0264417767850.6340236944460.05979665902120.666811638454-0.00377541486201-0.00354591797570.673346082119-0.07151477169260.9737642183995.56225641921-28.6330958222-17.4352071234
34.9651220412.09958611793-2.514071283214.68383058927-2.402770478165.79876827126-0.1500450161110.09636926621820.1248426382350.8844212914690.134586681899-0.736028873421-1.164100948440.1968735169680.3788042094960.568528839519-0.0189834442064-0.1770732238960.528022834509-0.01569255548080.8354695801711.91657330904-22.0075109314-14.2649825056
47.491720575360.0552374638110.2795646079621.75359612259-0.2731189484793.90590932103-0.1289729015540.1941674196830.0566995143961-0.160784164966-0.0005682172637610.1355241839450.104199296997-0.1873360123580.08371252445240.56988556581-0.03980710087880.01472837375430.495509936168-0.01831740267750.570389489169-5.06517310584-19.4835563912-26.058278051
58.66291932119-0.2316420086040.4762727973724.692359956321.901214101546.605068885620.0958330777462-0.6537265222410.09735887367220.567363835471-0.1812353591680.3026640600340.219462186064-0.1692401735530.1176232825980.602437407912-0.0975064093510.01787902508320.5927537172440.02093138392880.78289135416330.0787816451-31.7283821965-29.0351489624
60.6643489447672.31950887378-2.360149740248.37850979314-8.281528664238.36023654271-0.04147740156651.946258563382.21140048391-0.919695278928-0.13342117883-1.28381132744-3.062437795011.18333180182-0.3160141635681.65269081124-0.424216996054-0.0996904536871.11789544820.4164916197221.7147765491640.0013226949-14.7700557628-30.7837520258
73.20162080546-1.0409506056-0.9637000785211.76824417633-1.467064264712.456358359110.0509762602560.6396997821860.741613939727-1.3098277260.2004683227310.195924952988-0.313274248544-0.169499515537-0.5206581484841.17284954387-0.2103795316860.02496153083250.7655003122090.1796350040471.1747614754630.8755951295-18.1631049094-32.8743391906
89.338811734063.410615426790.7513002917318.72526016822-7.199575782097.53223686291-0.1106890117491.573247590680.9094971123551.65346425204-1.052258283091.28534679678-3.187540751690.6959914931411.315444140971.23142604706-0.2825299201250.1628510323890.9882650802310.05995774213731.4847588791736.4242622903-12.384226824-23.3939587276
92.66654517321-2.264976503673.554190013544.51410651053-3.66169312054.90197576713-0.833803383285-0.6190496507631.909082003851.24021835386-0.05533031453780.228956821734-2.09952764312-0.7512884168990.5024477672541.16910342651-0.0511188192920.104260069510.581026914150.1150571081561.4495941213526.7892292887-12.270844112-27.2055025491
105.63621910363-3.35250697682.865713904594.590630720090.3978611968838.03152870975-0.382678545815-0.4745903558191.562739334390.382540703836-0.0518097510751-0.164910250704-0.813955246330.2701351275890.478978171150.664017889828-0.1172295937190.0953643965310.554038477135-0.04417050262021.0212179904428.2835990272-24.6461774961-16.0438468443
113.565110183422.718680672743.947621454873.966683216591.239454231756.38443779949-0.7587798606781.165227044692.07477084298-1.00860321508-0.0461691122724-0.121263672809-0.7440174783510.7236823118240.9235735742350.83057795776-0.1263670577110.01084256493190.6339447687470.09871658787021.0374127305232.6415493122-24.116246294-26.3989124779
123.43283019534-1.47957778836-1.863644730774.76589415142-0.3738758592683.591816577570.006580139978960.03954900010080.226898723737-0.3943848906970.06883738130450.2288222380010.1348632808930.277865279216-0.1855915907430.651969419556-0.1246352848980.05685131973860.7225400303190.0645354068390.8553977372435.6056231228-35.9477798328-21.1570952005
132.18353254422-0.436098834401-0.1816029340644.30282358294-0.8343689806223.422499667590.33814175428-0.0923677736699-0.3495795851590.124865783169-0.226330157196-0.30242842441-0.2751250356890.161973808760.2798141653920.761037937755-0.153161897673-0.002704932999820.831661238464-0.02678016942370.92069984459635.2735944888-34.999438592-15.4613790881
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 47 )AA9 - 471 - 38
22chain 'A' and (resid 48 through 94 )AA48 - 9439 - 85
33chain 'A' and (resid 95 through 109 )AA95 - 10986 - 100
44chain 'A' and (resid 110 through 160 )AA110 - 160101 - 151
55chain 'B' and (resid 9 through 21 )BB9 - 211 - 13
66chain 'B' and (resid 22 through 29 )BB22 - 2914 - 21
77chain 'B' and (resid 30 through 47 )BB30 - 4722 - 39
88chain 'B' and (resid 48 through 54 )BB48 - 5440 - 46
99chain 'B' and (resid 55 through 67 )BB55 - 6747 - 59
1010chain 'B' and (resid 68 through 94 )BB68 - 9460 - 86
1111chain 'B' and (resid 95 through 109 )BB95 - 10987 - 101
1212chain 'B' and (resid 110 through 136 )BB110 - 136102 - 128
1313chain 'B' and (resid 137 through 160 )BB137 - 160129 - 152

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