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- PDB-6kan: Crystal structure of FKRP in complex with Ba ion -

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Basic information

Entry
Database: PDB / ID: 6kan
TitleCrystal structure of FKRP in complex with Ba ion
ComponentsFukutin-related protein
KeywordsTRANSFERASE / glycosyltranferase / phospho ribitoyl tranferase
Function / homology
Function and homology information


pentitol metabolic process / filtration diaphragm assembly / pentose metabolic process / connective tissue development / creatine metabolic process / connective tissue replacement / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phosphotransferase activity, for other substituted phosphate groups / oxygen metabolic process / localization of cell ...pentitol metabolic process / filtration diaphragm assembly / pentose metabolic process / connective tissue development / creatine metabolic process / connective tissue replacement / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phosphotransferase activity, for other substituted phosphate groups / oxygen metabolic process / localization of cell / maintenance of protein localization in endoplasmic reticulum / protein O-linked mannosylation / diaphragm development / skeletal muscle fiber differentiation / basement membrane organization / dystroglycan binding / glial cell differentiation / reelin-mediated signaling pathway / respiratory system process / skeletal muscle tissue regeneration / protein import / camera-type eye development / response to alcohol / adult walking behavior / neuromuscular process / bone mineralization / skeletal muscle myofibril / heart morphogenesis / response to glucocorticoid / rough endoplasmic reticulum / laminin binding / muscle contraction / response to activity / glycolytic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tetramerization / brain development / sarcolemma / protein processing / lipid metabolic process / neuron migration / in utero embryonic development / inflammatory response / response to xenobiotic stimulus / Golgi membrane / Golgi apparatus / extracellular space / nucleoplasm / metal ion binding / identical protein binding / cytosol
Similarity search - Function
LicD family / : / : / LicD family / Fukutin-related protein stem domain
Similarity search - Domain/homology
: / Ribitol 5-phosphate transferase FKRP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsKuwabara, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K07284 Japan
Japan Society for the Promotion of Science26840029 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy.
Authors: Kuwabara, N. / Imae, R. / Manya, H. / Tanaka, T. / Mizuno, M. / Tsumoto, H. / Kanagawa, M. / Kobayashi, K. / Toda, T. / Senda, T. / Endo, T. / Kato, R.
History
DepositionJun 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fukutin-related protein
B: Fukutin-related protein
C: Fukutin-related protein
D: Fukutin-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,60420
Polymers200,1074
Non-polymers2,49716
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-64 kcal/mol
Surface area73980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.073, 119.051, 257.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fukutin-related protein / Ribitol-5-phosphate transferase


Mass: 50026.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKRP / Cell line (production host): HEK293S GnT- / Production host: Homo sapiens (human) / References: UniProt: Q9H9S5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4-8% PEG 4,000, 0.1 M HEPES-NaOH (pH7.5),0.5 M LiCl2, and 20 mM BaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.92 Å / Num. obs: 112891 / % possible obs: 99.82 % / Redundancy: 7.4 % / Net I/σ(I): 14.47
Reflection shellResolution: 2.2508→2.2764 Å / Num. unique obs: 3410

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.251→48.918 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.64
RfactorNum. reflection% reflection
Rfree0.2318 5680 5.03 %
Rwork0.1957 --
obs0.1975 112891 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.251→48.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13541 0 107 484 14132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114024
X-RAY DIFFRACTIONf_angle_d1.04919230
X-RAY DIFFRACTIONf_dihedral_angle_d7.3228287
X-RAY DIFFRACTIONf_chiral_restr0.0542147
X-RAY DIFFRACTIONf_plane_restr0.0072543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2508-2.27640.40631820.34363410X-RAY DIFFRACTION96
2.2764-2.30310.3481940.31143497X-RAY DIFFRACTION100
2.3031-2.33120.3471810.29753590X-RAY DIFFRACTION100
2.3312-2.36070.34751700.27833519X-RAY DIFFRACTION100
2.3607-2.39180.3011890.27143540X-RAY DIFFRACTION100
2.3918-2.42460.31341960.26323528X-RAY DIFFRACTION100
2.4246-2.45920.30521720.25273540X-RAY DIFFRACTION100
2.4592-2.49590.27831860.23563561X-RAY DIFFRACTION100
2.4959-2.53490.27952180.2343521X-RAY DIFFRACTION100
2.5349-2.57650.27871590.23643589X-RAY DIFFRACTION100
2.5765-2.62090.29891980.2433507X-RAY DIFFRACTION100
2.6209-2.66850.30691830.23533572X-RAY DIFFRACTION100
2.6685-2.71990.27111770.23663539X-RAY DIFFRACTION100
2.7199-2.77540.27841740.22883591X-RAY DIFFRACTION100
2.7754-2.83570.27152020.21613545X-RAY DIFFRACTION100
2.8357-2.90170.27711890.21963551X-RAY DIFFRACTION100
2.9017-2.97420.26991860.2163571X-RAY DIFFRACTION100
2.9742-3.05460.27781850.23173544X-RAY DIFFRACTION100
3.0546-3.14450.2652000.22953546X-RAY DIFFRACTION100
3.1445-3.2460.2851900.22973573X-RAY DIFFRACTION100
3.246-3.3620.25132050.21113591X-RAY DIFFRACTION100
3.362-3.49650.26621990.2043562X-RAY DIFFRACTION100
3.4965-3.65560.23631720.19713600X-RAY DIFFRACTION100
3.6556-3.84830.21041850.18293617X-RAY DIFFRACTION100
3.8483-4.08930.18962040.16143565X-RAY DIFFRACTION100
4.0893-4.40480.16381940.15163627X-RAY DIFFRACTION100
4.4048-4.84780.16282040.14153605X-RAY DIFFRACTION100
4.8478-5.54840.19141840.15683682X-RAY DIFFRACTION100
5.5484-6.98710.20962040.18383695X-RAY DIFFRACTION100
6.9871-48.92950.19131980.16393833X-RAY DIFFRACTION99
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)
11.50260.47070.23071.90940.21331.73630.0086-0.1360.0506-0.0046-0.07090.3899-0.0725-0.43150.05420.30730.05150.02740.4142-0.00780.3533-5.9251240.934237.7986
21.8655-0.87280.95243.44930.25613.4514-0.0758-0.13070.28270.62010.1417-1.04620.06260.5033-0.06370.40180.0435-0.15070.4143-0.02040.567731.5816244.580563.0114
32.04740.9520.37352.64450.47482.0368-0.02390.3942-0.243-0.58840.1707-0.6215-0.1560.3581-0.12550.4630.00580.12530.3655-0.04960.445724.2617244.822417.2664
40.86451.60140.24813.77210.85120.660.2517-0.1352-0.29070.1312-0.0345-0.75160.11740.1218-0.23890.45690.0251-0.08190.3381-0.02370.503113.8217217.526220.6573
52.15840.08450.71773.8472-0.51534.26610.1196-0.2091-0.31490.08680.03940.40290.4248-0.5469-0.13410.4651-0.0329-0.07210.35370.01980.4923-1.1191199.018915.8704
61.505-0.09810.30942.9228-0.20592.2388-0.05530.2599-0.0075-0.3031-0.1874-0.7111-0.03470.63560.27860.37490.0110.08490.51470.12050.508947.6287281.494127.9835
71.97830.1030.28082.1156-0.62791.9613-0.062-0.1776-0.19160.0936-0.1976-0.61510.14140.57810.230.31410.046-0.02340.45930.05750.448844.7339272.442543.336
81.84660.8481-0.11211.9346-0.39251.3219-0.0714-0.18360.29170.4185-0.1579-0.1626-0.33430.26170.23030.3717-0.0185-0.11840.4315-0.01550.329533.403285.169248.7329
91.5292-0.2671-0.58922.74310.02662.4491-0.0179-0.1329-0.00870.40410.0010.3621-0.0562-0.17610.05130.33340.02790.03870.3579-0.01670.319310.7242275.722961.6489
102.63530.1933-1.52263.373-0.95323.16120.0786-0.08860.23330.52950.06340.7772-0.4023-0.6256-0.04560.52740.10080.08060.5003-0.05950.49262.1286284.54363.828
111.4589-0.1122-0.42462.43870.50132.537-0.185-0.2727-0.33220.68010.04630.61970.3189-0.30630.14090.54440.01120.15580.46210.02180.46765.2238264.391467.6861
122.7164-0.8588-0.58874.0956-0.22.6217-0.00220.3177-0.2109-0.26660.13260.53860.3277-0.3785-0.06550.3903-0.0511-0.04830.37380.02540.32697.7416269.673324.2635
131.3827-1.236-0.19711.4122-0.4131.3498-0.1854-0.04670.0502-0.07710.067-0.06850.02810.04590.03620.2889-0.02140.0130.2404-0.02920.284816.2831268.765933.9435
142.0008-1.762-0.65052.8827-0.79362.56830.01190.5451-0.1533-0.5321-0.08240.19220.3955-0.1914-0.02570.4481-0.0208-0.00850.2911-0.03270.295214.3007269.452820.0463
151.81810.9424-0.26652.3749-0.32921.1056-0.260.3970.1443-0.74980.22740.3704-0.0345-0.2519-0.01890.5920.0006-0.1270.43270.02770.368513.5226281.584412.5987
167.42761.9775-3.17882.8534-0.92932.51460.3118-0.03170.29420.1551-0.13140.5342-0.4746-0.1935-0.09880.52920.0628-0.06190.35830.01050.413411.9493290.550129.8874
172.34890.48-0.70953.1822-0.29771.60250.2561-0.07420.1262-0.0081-0.16430.0425-0.12960.14580.0320.55510.0204-0.04180.3040.04140.272328.7668301.322921.9283
181.8044-0.061-0.29992.6701-1.04863.03940.3117-0.33970.48290.3813-0.1084-0.098-0.78970.4007-0.17210.6128-0.15590.07820.4167-0.05710.428332.1956319.753219.2856
191.78590.4872-0.33082.5237-1.413.12220.3516-0.38770.45340.3898-0.2456-0.3462-0.7870.9076-0.07980.7501-0.22860.06160.5594-0.05580.51637.4282322.391319.7227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 289 )
2X-RAY DIFFRACTION2chain 'A' and (resid 290 through 493 )
3X-RAY DIFFRACTION3chain 'B' and (resid 47 through 250 )
4X-RAY DIFFRACTION4chain 'B' and (resid 251 through 336 )
5X-RAY DIFFRACTION5chain 'B' and (resid 337 through 490 )
6X-RAY DIFFRACTION6chain 'C' and (resid 47 through 140 )
7X-RAY DIFFRACTION7chain 'C' and (resid 141 through 250 )
8X-RAY DIFFRACTION8chain 'C' and (resid 251 through 289 )
9X-RAY DIFFRACTION9chain 'C' and (resid 290 through 374 )
10X-RAY DIFFRACTION10chain 'C' and (resid 375 through 423 )
11X-RAY DIFFRACTION11chain 'C' and (resid 424 through 493 )
12X-RAY DIFFRACTION12chain 'D' and (resid 47 through 83 )
13X-RAY DIFFRACTION13chain 'D' and (resid 84 through 111 )
14X-RAY DIFFRACTION14chain 'D' and (resid 112 through 139 )
15X-RAY DIFFRACTION15chain 'D' and (resid 140 through 250 )
16X-RAY DIFFRACTION16chain 'D' and (resid 251 through 272 )
17X-RAY DIFFRACTION17chain 'D' and (resid 273 through 315 )
18X-RAY DIFFRACTION18chain 'D' and (resid 316 through 374 )
19X-RAY DIFFRACTION19chain 'D' and (resid 375 through 485 )

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