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- PDB-5k24: Crystal structure of the complex between phosphatase PRL-2 in the... -

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Basic information

Entry
Database: PDB / ID: 5k24
TitleCrystal structure of the complex between phosphatase PRL-2 in the oxidized state with the Bateman domain of murine magnesium transporter CNNM3
Components
  • Metal transporter CNNM3
  • Protein tyrosine phosphatase type IVA 2
KeywordsHYDROLASE/TRANSPORTER PROTEIN/PROTEIN BINDING / Complex / phosphatase / magnesium transporter / protein binding / HYDROLASE / HYDROLASE-TRANSPORTER PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


RAB geranylgeranylation / magnesium ion homeostasis / transmembrane transporter activity / monoatomic ion transport / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / early endosome / nucleus / plasma membrane / 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
CITRATE ANION / Protein tyrosine phosphatase type IVA 2 / Metal transporter CNNM3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsKozlov, G. / Gulerez, I. / Gehring, K.
CitationJournal: Sci Rep / Year: 2017
Title: PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3.
Authors: Zhang, H. / Kozlov, G. / Li, X. / Wu, H. / Gulerez, I. / 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 / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein tyrosine phosphatase type IVA 2
B: Protein tyrosine phosphatase type IVA 2
C: Metal transporter CNNM3
D: Metal transporter CNNM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6595
Polymers76,4704
Non-polymers1891
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-21 kcal/mol
Surface area28040 Å2
Unit cell
Length a, b, c (Å)154.222, 52.119, 102.855
Angle α, β, γ (deg.)90.00, 106.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-501-

FLC

21D-501-

FLC

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 152
2010B5 - 152
1020C318 - 451
2020D318 - 451

NCS ensembles :
ID
1
2

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Components

#1: Protein Protein tyrosine phosphatase type IVA 2 / Protein-tyrosine phosphatase 4a2 / Protein-tyrosine phosphatase of regenerating liver 2 / PRL-2


Mass: 20893.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptp4a2, Prl2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O70274, protein-tyrosine-phosphatase
#2: Protein Metal transporter CNNM3 / Ancient conserved domain-containing protein 3 / mACDP3 / Cyclin-M3


Mass: 17341.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnnm3, Acdp3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q32NY4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium citrate, 19% PEG 3350, 10 mM L-cysteine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9773 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2014
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9773 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13689 / % possible obs: 98.88 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 33.9
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.881 / SU B: 64.728 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.552
RfactorNum. reflection% reflectionSelection details
Rfree0.30327 740 5.1 %RANDOM
Rwork0.25242 ---
obs0.25534 13689 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 121.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20.8 Å2
2--0.98 Å20 Å2
3----2.01 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4509 0 13 0 4522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8371.9786289
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_restr0.0460.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213493
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_it1.5076.362288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6399.5412853
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3896.4492332
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.57263.3995891
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1860.1
12B1860.1
21C1910.06
22D1910.06
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 37 -
Rwork0.339 913 -
obs--90.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.0628-1.204-2.21363.91570.95274.5463-0.1826-0.44080.22170.59260.26250.108-0.2491-0.1872-0.07990.51630.0125-0.17010.27160.00960.4812134.131223.4234-35.3434
24.60110.32493.268810.28041.57532.5778-0.0617-0.23180.13861.1220.13750.44980.1703-0.1019-0.07580.48410.0085-0.10920.1655-0.06570.6646129.694624.7535-38.5357
30.99471.7543-1.40488.26971.12634.78130.00420.12710.15630.0924-0.0790.341-0.2066-0.31220.07480.40750.0012-0.20670.19610.01290.481126.509522.8879-44.9757
44.07370.32270.83788.7365-1.54695.2027-0.12340.24590.391-0.80850.0940.007-0.4780.36110.02930.4433-0.0521-0.05390.32460.03450.5397138.794221.5797-51.8791
53.48970.6237-0.3086.5726-2.57632.0242-0.0848-0.25520.32150.22460.02510.0123-0.11490.21890.05970.4295-0.0513-0.15050.2433-0.00630.4748138.714319.9276-42.6568
611.3046-13.184911.980917.8083-17.713118.58660.47410.05690.3875-0.3097-0.7856-0.44040.37341.29190.31150.55390.0214-0.1920.46840.05430.6936152.431515.3062-44.9627
76.8568-3.12893.81155.0795-5.1299.7531-0.4675-0.73440.41250.6986-0.1442-0.0394-0.67480.38580.61170.33050.0086-0.16570.404-0.01650.5098145.6913.1185-34.648
87.43824.0633-3.110516.4167-4.1987.4074-0.15030.56040.0707-1.6109-0.3154-0.92620.52640.61890.46570.3280.1041-0.06450.29910.00260.478146.12929.3547-49.3219
919.161-8.3036-9.43387.95244.81534.76890.15250.8411-1.5383-1.943-0.89420.7527-0.3648-0.51450.74171.2758-0.2146-0.13410.6138-0.17620.553145.8145-13.138127.4952
104.95295.44421.04476.10091.08170.30560.29810.17430.36030.5736-0.09890.6011-0.01440.1078-0.19910.736-0.60620.15821.018-0.26490.9701130.5103-9.173227.9096
1138.89882.673317.73043.3335-8.244936.5289-1.1134-2.1015-0.80090.52421.2028-0.1776-2.3722-4.975-0.08940.6287-0.11830.37931.1573-0.20670.6042133.702-6.901536.7495
1273.63915.470348.31850.63293.470331.78120.5872-1.8530.6672-0.2115-0.80190.31950.5873-0.91860.21471.69660.49390.16562.1161-0.56571.2725125.8798-12.757836.5062
139.8187-1.14082.90559.4796-2.63261.44650.5038-1.1709-1.4264-0.3852-0.10750.21190.3641-0.3688-0.39630.8088-0.51940.17190.42860.0190.2957142.3112-10.812341.1786
1412.12393.74141.1542.15623.619710.859-0.23740.0768-0.54590.1504-0.34980.09640.545-1.16320.58730.5753-0.36460.15330.46490.04270.7311144.5332-4.358634.5236
159.4838-0.59080.387611.0954-0.767211.6346-0.06810.824-0.2648-0.2642-0.1292-0.15760.91420.17170.19720.4014-0.1684-0.00770.4267-0.08220.4688152.5534-1.100229.8585
1617.15975.15283.16941.57761.02750.77630.2866-1.4546-0.70110.1869-0.3575-0.13610.3096-0.08630.07091.03750.1180.030.46840.16080.4122156.5505-3.885741.408
1711.9299-2.6421-3.55413.92430.80384.6142-0.12120.1488-0.80350.0222-0.15670.38910.348-0.55990.27790.3015-0.0239-0.10430.52940.05020.4263126.51021.6509-12.563
188.23831.614-5.81435.6041-3.072116.5269-0.061-0.33470.24680.0903-0.0815-0.31950.3375-0.84990.14250.31990.0842-0.10140.60830.07840.6068123.70634.416-13.1341
197.5446-4.6635-2.91810.638412.824531.02190.1146-0.59770.1290.26410.223-0.1098-0.6326-1.1161-0.33760.2452-0.0608-0.01480.5240.07970.5013124.224610.9964-13.3356
2019.6064-5-4.616712.90681.91181.14680.45261.63761.57211.4983-0.17261.44070.0092-0.4849-0.280.57140.1879-0.01831.29960.18880.7171113.255714.5042-10.1857
213.9117-1.489-0.00610.8309-0.50884.65440.2034-0.67440.37250.02320.00140.0186-0.59040.5831-0.20480.3121-0.0746-0.10440.68240.04870.6113138.478711.3117-16.5306
2273.3684-12.685-7.106670.344110.33871.911-1.55370.20892.152-0.42231.41491.99060.06570.21560.13870.66660.2791-0.18151.09250.25110.3802138.882315.8331-11.4722
233.8117-0.11431.59960.9328-1.546416.25880.0613-0.2859-0.0591-0.03690.04830.04380.60630.0241-0.10960.37460.0311-0.04530.29940.05820.5115136.11514.1221-25.2194
2419.0171-9.5463-4.583433.19415.94971.58890.0538-1.7364-0.00891.31180.0993-0.86850.19410.2268-0.1530.3688-0.1028-0.17690.87020.18270.2911144.7731.8371-5.1291
250.9512-1.73880.47125.59872.52917.4301-0.1765-0.13910.0962-0.8464-0.12080.8954-1.7843-0.61170.29730.7517-0.0808-0.56350.5993-0.05251.1476126.033414.211711.6711
2612.0275-36.087520.6904108.647-62.02135.6304-1.4984-1.4836-1.83823.78344.54446.0182-2.711-2.2943-3.0461.90340.2193-0.81942.58370.56181.0075122.879713.59423.2195
2711.8537-10.2751-11.085928.55298.206125.4321-0.3007-0.31950.0720.5258-0.44781.0557-1.4006-0.52780.74850.3473-0.2252-0.06210.7735-0.0970.5927124.93929.165115.9346
287.22841.9313-2.20218.1871-1.22447.4277-0.2760.08610.3961-1.04290.11891.5533-0.3824-1.07280.15710.2097-0.0618-0.24760.69830.04010.6426119.2034.631512.4298
293.6659-4.2108-0.06327.4855-3.07638.3794-0.14880.0714-0.63380.3650.544-0.21950.66910.2815-0.39520.3111-0.0741-0.40021.1165-0.39791.0021135.76453.360412.8897
3025.7201-24.239514.808823.6603-20.324458.4465-0.44490.8145-0.64260.2238-0.6090.37331.0394-0.64031.05390.5170.04230.34410.9074-0.13880.846143.99762.76125.8617
314.7882-1.83355.42650.9763-0.42319.51290.06640.1047-0.07980.00310.05220.0687-0.1981-0.1921-0.11870.2952-0.1994-0.01240.69150.06390.5122139.48569.193119.4256
329.75629.788-6.756310.6089-7.92747.9504-0.53430.56491.1613-0.54670.37640.4886-0.6132-0.68870.15780.72710.17880.00170.60030.15280.7422142.114513.959-0.1544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 31
2X-RAY DIFFRACTION2A32 - 50
3X-RAY DIFFRACTION3A51 - 70
4X-RAY DIFFRACTION4A71 - 90
5X-RAY DIFFRACTION5A91 - 117
6X-RAY DIFFRACTION6A118 - 126
7X-RAY DIFFRACTION7A127 - 138
8X-RAY DIFFRACTION8A139 - 154
9X-RAY DIFFRACTION9B5 - 15
10X-RAY DIFFRACTION10B16 - 38
11X-RAY DIFFRACTION11B39 - 49
12X-RAY DIFFRACTION12B50 - 60
13X-RAY DIFFRACTION13B61 - 96
14X-RAY DIFFRACTION14B97 - 118
15X-RAY DIFFRACTION15B119 - 144
16X-RAY DIFFRACTION16B145 - 153
17X-RAY DIFFRACTION17C317 - 347
18X-RAY DIFFRACTION18C348 - 362
19X-RAY DIFFRACTION19C363 - 374
20X-RAY DIFFRACTION20C375 - 391
21X-RAY DIFFRACTION21C392 - 410
22X-RAY DIFFRACTION22C411 - 417
23X-RAY DIFFRACTION23C418 - 443
24X-RAY DIFFRACTION24C444 - 453
25X-RAY DIFFRACTION25D318 - 347
26X-RAY DIFFRACTION26D348 - 353
27X-RAY DIFFRACTION27D354 - 360
28X-RAY DIFFRACTION28D361 - 390
29X-RAY DIFFRACTION29D391 - 405
30X-RAY DIFFRACTION30D406 - 414
31X-RAY DIFFRACTION31D415 - 443
32X-RAY DIFFRACTION32D444 - 452

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