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- PDB-5k22: Crystal structure of the complex between human PRL-2 phosphatase ... -

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Basic information

Entry
Database: PDB / ID: 5k22
TitleCrystal structure of the complex between human PRL-2 phosphatase in reduced state and Bateman domain of human CNNM3
Components
  • Metal transporter CNNM3
  • Protein tyrosine phosphatase type IVA 2
KeywordsTRANSPORT PROTEIN/PROTEIN BINDING / alpha-beta fold / complex / protein binding / phosphatase / TRANSPORT PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


magnesium ion homeostasis / RAB geranylgeranylation / enzyme inhibitor activity / transmembrane transporter activity / monoatomic ion transport / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity ...magnesium ion homeostasis / RAB geranylgeranylation / enzyme inhibitor activity / transmembrane transporter activity / monoatomic ion transport / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / early endosome / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ancient conserved domain protein family / CNNM, transmembrane domain / CNNM transmembrane domain profile. / : / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / CBS domain superfamily ...Ancient conserved domain protein family / CNNM, transmembrane domain / CNNM transmembrane domain profile. / : / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase 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 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein tyrosine phosphatase type IVA 2 / Metal transporter CNNM3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsKozlov, G. / Wu, H. / Gehring, K.
CitationJournal: EMBO Rep. / Year: 2016
Title: Phosphocysteine in the PRL-CNNM pathway mediates magnesium homeostasis.
Authors: Gulerez, I. / Funato, Y. / Wu, H. / Yang, M. / Kozlov, G. / Miki, H. / Gehring, K.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine phosphatase type IVA 2
B: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)38,4312
Polymers38,4312
Non-polymers00
Water1086
1
A: Protein tyrosine phosphatase type IVA 2
B: Metal transporter CNNM3

A: Protein tyrosine phosphatase type IVA 2
B: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)76,8624
Polymers76,8624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
2
A: Protein tyrosine phosphatase type IVA 2


Theoretical massNumber of molelcules
Total (without water)20,7971
Polymers20,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8050 Å2
MethodPISA
3
B: Metal transporter CNNM3

B: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)35,2682
Polymers35,2682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2430 Å2
ΔGint-29 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.447, 126.717, 152.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Protein tyrosine phosphatase type IVA 2 / HU-PP-1 / OV-1 / PTP(CAAXII) / Protein-tyrosine phosphatase 4a2 / Protein-tyrosine phosphatase of ...HU-PP-1 / OV-1 / PTP(CAAXII) / Protein-tyrosine phosphatase 4a2 / Protein-tyrosine phosphatase of regenerating liver 2 / PRL-2


Mass: 20796.859 Da / Num. of mol.: 1 / Mutation: C95A, C96A, C119A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP4A2, PRL2, PTPCAAX2, BM-008 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q12974, protein-tyrosine-phosphatase
#2: Protein Metal transporter CNNM3 / Ancient conserved domain-containing protein 3 / Cyclin-M3


Mass: 17634.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM3, ACDP3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NE01
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.42 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.8 M succinic acid, 30% w/v D-(+)-glucose monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6307 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 12, 2015
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6307 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 10215 / % possible obs: 98.91 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 38.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 10 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 3.1 / % possible all: 93.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.92 / SU B: 40.27 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 1.543 / ESU R Free: 0.411
RfactorNum. reflection% reflectionSelection details
Rfree0.27431 601 5.6 %RANDOM
Rwork0.23142 ---
obs0.23366 10215 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 95.826 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2---4.17 Å20 Å2
3---0.8 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 0 6 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192470
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7941.9753356
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211874
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4335.1341218
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7857.71519
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3645.1761250
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined2.85451.4483013
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.003→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 36 -
Rwork0.346 685 -
obs--93.88 %
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)
111.54660.6817-0.21275.521-3.639810.05330.2690.604-0.2649-0.5937-0.172-0.296-0.21110.602-0.0970.53060.11620.11290.4456-0.26680.331610.778534.6101173.4692
29.0408-1.69351.0694.8007-4.62659.53040.1087-1.2495-0.62130.71190.0847-0.4707-0.45930.3938-0.19350.49850.1046-0.02060.5384-0.0980.378510.356332.3189184.2315
35.6038-0.8109-3.18655.9757-1.184719.9685-0.2206-0.8837-0.50760.21070.0879-1.75870.11381.10810.13270.40580.0579-0.05290.6233-0.13480.734715.908337.0274183.5847
45.02461.84116.2547.27944.57669.64610.2482-1.00590.02791.2524-0.08580.03320.4116-0.3173-0.16240.5841-0.04390.06211.0045-0.22190.27945.020638.0593188.8722
53.03463.26420.455712.7812.0344.01940.07720.24010.1369-0.4144-0.00810.1541-0.5672-0.1302-0.06910.34180.1695-0.00690.3724-0.15830.3122-3.413841.8654177.7693
64.8863-0.8373-0.50058.10790.91936.93890.04540.64850.2469-1.24110.0577-0.1534-0.2940.0317-0.10310.48260.1115-0.0020.4298-0.12390.35533.691637.1331170.9742
76.8592-4.5557-1.78997.47224.69574.6532-0.04111.0136-0.0871-1.1603-0.34110.3174-0.2183-0.31390.38220.7795-0.0877-0.0950.5202-0.10690.274-1.247329.7594167.3546
81.6482-3.9541-1.528710.09422.72032.98820.34680.14180.1387-0.8636-0.4198-0.3593-0.32740.24850.0730.84310.0588-0.12940.84320.2890.5455-3.789648.5409165.189
93.43543.34682.30973.97174.603212.0556-0.3873-0.20440.1557-0.0448-0.16460.61890.1837-0.83980.5520.52270.19970.42250.3470.25580.87322.5117-1.592157.613
103.5869-0.97131.50293.2503-0.56348.69710.094-0.2067-0.39270.0427-0.13230.33660.2811-0.40570.03830.2471-0.08910.05090.1649-0.09480.408314.67662.8497183.57
115.8074-2.91773.30515.4962-0.04074.8669-0.0613-0.35280.17610.3251-0.05880.19430.0309-0.21860.12010.3984-0.12130.04220.1917-0.07810.276318.18618.7825188.7114
123.8666-2.16451.70132.77810.30337.1568-0.1135-0.04740.18850.1889-0.1091-0.0645-0.32140.24820.22270.3926-0.13010.02760.1711-0.11130.375319.633512.0712184.2762
135.5318-0.0281-13.56620.2573-0.538734.73320.6009-0.14610.4044-0.4027-0.2051-0.2414-0.56070.9999-0.39590.86720.09830.12671.04910.39420.735625.977613.7819170.9284
141.6381-1.3544-0.75324.7655-0.48634.45470.27160.7318-0.06740.1554-0.56630.748-0.247-0.34410.29480.46450.0297-0.03720.4071-0.11660.46146.765716.0395174.6508
158.0678-5.11320.16627.5721-2.40635.27590.44730.1561-0.8073-0.29-0.41390.9416-0.0901-0.1568-0.03340.3388-0.0261-0.04140.1621-0.18190.476811.28610.1968175.3914
1610.2997-9.1191-1.308724.201813.04998.9431-0.45180.0073-1.17580.94230.06531.4070.50670.09330.38650.5949-0.0088-0.01220.378-0.03260.532721.4705-1.3876168.3095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 29
3X-RAY DIFFRACTION3A30 - 39
4X-RAY DIFFRACTION4A40 - 64
5X-RAY DIFFRACTION5A65 - 90
6X-RAY DIFFRACTION6A91 - 130
7X-RAY DIFFRACTION7A131 - 149
8X-RAY DIFFRACTION8A150 - 156
9X-RAY DIFFRACTION9B298 - 309
10X-RAY DIFFRACTION10B310 - 345
11X-RAY DIFFRACTION11B346 - 371
12X-RAY DIFFRACTION12B372 - 404
13X-RAY DIFFRACTION13B405 - 409
14X-RAY DIFFRACTION14B410 - 428
15X-RAY DIFFRACTION15B429 - 437
16X-RAY DIFFRACTION16B438 - 446

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