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- PDB-6kal: Crystal structure of FKRP in complex with Mg ion and CMP -

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Basic information

Entry
Database: PDB / ID: 6kal
TitleCrystal structure of FKRP in complex with Mg ion and CMP
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 / diaphragm development / maintenance of protein localization in endoplasmic reticulum / protein O-linked glycosylation via mannose / skeletal muscle fiber differentiation / basement membrane organization / dystroglycan binding / glial cell differentiation / reelin-mediated signaling pathway / skeletal muscle tissue regeneration / respiratory system process / protein import / camera-type eye development / adult walking behavior / response to alcohol / neuromuscular process / bone mineralization / skeletal muscle myofibril / heart morphogenesis / laminin binding / rough endoplasmic reticulum / response to glucocorticoid / muscle contraction / glycolytic process / response to activity / protein tetramerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / brain development / sarcolemma / protein processing / lipid metabolic process / neuron migration / in utero embryonic development / response to xenobiotic stimulus / inflammatory response / 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
CYTIDINE-5'-MONOPHOSPHATE / Ribitol 5-phosphate transferase FKRP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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_conn_type / 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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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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)203,40527
Polymers200,1074
Non-polymers3,29723
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-128 kcal/mol
Surface area73580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.583, 118.674, 252.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 11 molecules ABCD

#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
#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

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Non-polymers , 4 types, 275 molecules

#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
#4: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.91 Å3/Da / Density % sol: 57.68 %
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) and 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.9962 Å / Num. obs: 72606 / % possible obs: 99.93 % / Redundancy: 6.7 % / Net I/σ(I): 13.56
Reflection shellResolution: 2.6→2.6342 Å / Num. unique obs: 2628

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.987 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.04
RfactorNum. reflection% reflection
Rfree0.2409 3680 5.07 %
Rwork0.1947 --
obs0.1971 72606 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13701 0 194 259 14154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114317
X-RAY DIFFRACTIONf_angle_d1.00219635
X-RAY DIFFRACTIONf_dihedral_angle_d7.4089991
X-RAY DIFFRACTIONf_chiral_restr0.0562187
X-RAY DIFFRACTIONf_plane_restr0.0092582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63420.38161360.332628X-RAY DIFFRACTION100
2.6342-2.67030.33661420.32632601X-RAY DIFFRACTION100
2.6703-2.70840.34631330.29842601X-RAY DIFFRACTION100
2.7084-2.74890.33881490.2762619X-RAY DIFFRACTION100
2.7489-2.79180.32021360.26282618X-RAY DIFFRACTION100
2.7918-2.83760.32871480.26032624X-RAY DIFFRACTION100
2.8376-2.88650.34271270.2592617X-RAY DIFFRACTION100
2.8865-2.9390.32331480.25762619X-RAY DIFFRACTION100
2.939-2.99550.27721360.2562627X-RAY DIFFRACTION100
2.9955-3.05660.34111380.25292622X-RAY DIFFRACTION100
3.0566-3.12310.28981290.23552653X-RAY DIFFRACTION100
3.1231-3.19570.2851450.23252610X-RAY DIFFRACTION100
3.1957-3.27560.2641470.22232607X-RAY DIFFRACTION100
3.2756-3.36420.28121550.21162660X-RAY DIFFRACTION100
3.3642-3.46320.25451330.21032614X-RAY DIFFRACTION100
3.4632-3.57490.25881300.20732663X-RAY DIFFRACTION100
3.5749-3.70260.21971420.19762651X-RAY DIFFRACTION100
3.7026-3.85080.23491580.18082643X-RAY DIFFRACTION100
3.8508-4.0260.20871230.17022653X-RAY DIFFRACTION100
4.026-4.23820.23881570.16212648X-RAY DIFFRACTION100
4.2382-4.50350.19271420.15112657X-RAY DIFFRACTION100
4.5035-4.85090.17791360.14462704X-RAY DIFFRACTION100
4.8509-5.33860.18561610.16042654X-RAY DIFFRACTION100
5.3386-6.10980.23241400.17892716X-RAY DIFFRACTION100
6.1098-7.69290.19611500.17372742X-RAY DIFFRACTION100
7.6929-48.99620.19031390.16142875X-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)
11.86810.98010.39432.01840.02662.3611-0.0455-0.08660.3167-0.0562-0.05570.4037-0.3925-0.55420.10650.56530.1376-0.00910.4527-0.01010.4435-8.0727241.915334.6439
23.61860.61772.41640.83881.21252.21120.0719-0.2214-0.12070.3163-0.0228-0.16150.0883-0.1422-0.03560.54180.04510.010.36040.04110.358515.3817236.890251.0235
35.2262-1.08812.87734.51441.00016.6635-0.0705-0.01170.27680.62340.186-1.12950.30571.0131-0.0680.58450.0274-0.10920.5260.02450.589535.7104241.584164.916
41.6702-0.3815-0.8471.1895-0.92255.5325-0.18680.17290.7658-0.07160.0218-0.7871-0.52410.3090.12530.8244-0.0953-0.12790.53260.03420.99328.8282255.944561.3593
51.98060.89580.44232.99720.36771.85640.04490.2687-0.1723-0.37250.1373-0.5535-0.1440.3014-0.14410.57480.0050.09970.3941-0.03040.490924.3801242.529617.4334
61.74050.44350.07396.03680.0132.92580.044-0.2079-0.19580.2512-0.0423-0.02440.2127-0.23030.01360.3530.015-0.04780.34390.03850.36332.0476202.979416.1555
71.63710.4563-0.51182.0673-0.06581.9765-0.0753-0.1955-0.13220.0552-0.1217-0.410.25370.44180.18240.48060.0609-0.03220.41540.07780.412744.1238277.363237.3283
82.2982-0.7418-1.70583.9157-0.09183.98930.0213-0.1029-0.08310.3757-0.06250.6363-0.1381-0.37060.0370.5403-0.03160.0330.4319-0.06480.41877.0161273.532563.03
92.70130.4637-0.2114.0585-0.31722.3803-0.12780.1273-0.1999-0.3120.20990.3770.4692-0.2505-0.07740.6366-0.0364-0.04640.36340.02680.38937.8611268.891823.5944
100.7798-0.08880.00111.5836-0.39541.263-0.04190.0163-0.08580.0199-0.0049-0.03270.0684-0.00280.03070.5338-0.0528-0.01420.312-0.04980.406416.3943267.992433.164
111.5201-0.4477-0.51062.6665-0.78331.6662-0.12980.6385-0.2486-0.41590.0310.20150.3912-0.11490.00180.7173-0.0261-0.04970.382-0.02440.345714.4091268.758219.3493
122.34921.1922-0.17942.9886-0.6781.3103-0.13840.30220.1267-0.56370.18840.40860.0127-0.1435-0.05430.65830.004-0.10540.41450.05120.413613.2345282.48815.2491
132.71150.7885-0.72883.3423-0.78462.1740.2626-0.2492-0.04830.0559-0.19830.0318-0.0510.1706-0.01040.48770.0042-0.03650.31810.02220.32228.6603300.555721.6083
142.63791.0718-0.60713.5908-0.83083.05810.3669-0.57010.41320.8047-0.2698-0.1413-0.80940.5539-0.12790.6788-0.1590.00170.4691-0.04040.411533.922320.530924.3312
152.89621.4755-0.39553.8049-0.4953.24860.0669-0.20520.22670.3858-0.1751-0.8457-0.77440.90840.03570.8271-0.21070.04040.5795-0.04380.692643.0902324.741315.0621
161.7277-0.76830.53014.8761-2.47733.06790.1460.10350.0172-0.511-0.4668-0.73460.1150.72940.35680.4889-0.01030.08520.45170.06460.450440.4845315.18578.9295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 250 )
2X-RAY DIFFRACTION2chain 'A' and (resid 251 through 336 )
3X-RAY DIFFRACTION3chain 'A' and (resid 337 through 454 )
4X-RAY DIFFRACTION4chain 'A' and (resid 455 through 492 )
5X-RAY DIFFRACTION5chain 'B' and (resid 47 through 272 )
6X-RAY DIFFRACTION6chain 'B' and (resid 273 through 491 )
7X-RAY DIFFRACTION7chain 'C' and (resid 47 through 289 )
8X-RAY DIFFRACTION8chain 'C' and (resid 290 through 492 )
9X-RAY DIFFRACTION9chain 'D' and (resid 47 through 83 )
10X-RAY DIFFRACTION10chain 'D' and (resid 84 through 111 )
11X-RAY DIFFRACTION11chain 'D' and (resid 112 through 139 )
12X-RAY DIFFRACTION12chain 'D' and (resid 140 through 272 )
13X-RAY DIFFRACTION13chain 'D' and (resid 273 through 315 )
14X-RAY DIFFRACTION14chain 'D' and (resid 316 through 428 )
15X-RAY DIFFRACTION15chain 'D' and (resid 429 through 454 )
16X-RAY DIFFRACTION16chain 'D' and (resid 455 through 491 )

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