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- PDB-6l7u: Crystal structure of FKRP in complex with Ba ion, Ba-SAD data -

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Basic information

Entry
Database: PDB / ID: 6l7u
TitleCrystal structure of FKRP in complex with Ba ion, Ba-SAD data
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 / response to alcohol / adult walking behavior / neuromuscular process / bone mineralization / skeletal muscle myofibril / heart morphogenesis / laminin binding / rough endoplasmic reticulum / muscle contraction / response to glucocorticoid / glycolytic process / response to activity / protein tetramerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / sarcolemma / brain development / 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
: / Ribitol 5-phosphate transferase FKRP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 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
DepositionNov 3, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 13, 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)202,02417
Polymers200,1074
Non-polymers1,91713
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-61 kcal/mol
Surface area74260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.147, 119.241, 255.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / Production host: Homo sapiens (human)
References: UniProt: Q9H9S5, Transferases; Glycosyltransferases; Pentosyltransferases
#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.: 5 / Source method: isolated from a natural 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.: 4 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4-8% PEG 4000, 0.1 M HEPES-NaOH (pH 7.5),0.5 M LiCl2, 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: 1.9 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.24→49.25 Å / Num. obs: 230030 / % possible obs: 99.9 % / Redundancy: 28.4 % / Biso Wilson estimate: 43.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.143 / Net I/σ(I): 22.4
Reflection shellResolution: 2.24→2.28 Å / Rmerge(I) obs: 3.288 / Num. unique obs: 5586 / CC1/2: 0.838 / Rrim(I) all: 3.352

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→49.24 Å / SU ML: 0.2841 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.7174 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2342 10983 5.01 %
Rwork0.2001 208064 -
obs0.2018 219047 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.56 Å2
Refinement stepCycle: LAST / Resolution: 2.24→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13531 0 78 499 14108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005213984
X-RAY DIFFRACTIONf_angle_d0.766619175
X-RAY DIFFRACTIONf_chiral_restr0.05552137
X-RAY DIFFRACTIONf_plane_restr0.00482538
X-RAY DIFFRACTIONf_dihedral_angle_d7.46168266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.270.46283380.45966992X-RAY DIFFRACTION99.31
2.27-2.290.31713550.29976879X-RAY DIFFRACTION99.64
2.29-2.320.31663700.28916927X-RAY DIFFRACTION99.92
2.32-2.350.32763730.28816917X-RAY DIFFRACTION99.67
2.35-2.380.30213450.28366906X-RAY DIFFRACTION99.83
2.38-2.410.30853490.27897018X-RAY DIFFRACTION99.85
2.41-2.450.30253670.26276881X-RAY DIFFRACTION99.83
2.45-2.480.26143580.24666993X-RAY DIFFRACTION99.9
2.48-2.520.26284060.24646851X-RAY DIFFRACTION99.92
2.52-2.560.2973400.23866957X-RAY DIFFRACTION99.95
2.56-2.610.30433530.24686927X-RAY DIFFRACTION100
2.61-2.660.32253940.23756985X-RAY DIFFRACTION99.96
2.66-2.710.22463360.22826922X-RAY DIFFRACTION99.96
2.71-2.760.25043560.22756962X-RAY DIFFRACTION99.93
2.76-2.820.25383550.22026927X-RAY DIFFRACTION99.93
2.82-2.890.29083880.23096902X-RAY DIFFRACTION99.95
2.89-2.960.29423710.24427007X-RAY DIFFRACTION99.95
2.96-3.040.29373450.23686893X-RAY DIFFRACTION100
3.04-3.130.27293870.236937X-RAY DIFFRACTION100
3.13-3.230.27723760.22336963X-RAY DIFFRACTION99.99
3.23-3.350.24373950.21346897X-RAY DIFFRACTION100
3.35-3.480.28354030.2156945X-RAY DIFFRACTION100
3.48-3.640.25423330.20146944X-RAY DIFFRACTION100
3.64-3.830.21873670.18126965X-RAY DIFFRACTION99.96
3.83-4.070.18683790.16476955X-RAY DIFFRACTION100
4.07-4.380.17543620.1546882X-RAY DIFFRACTION100
4.38-4.820.15773950.14516941X-RAY DIFFRACTION100
4.82-5.520.19633450.15346961X-RAY DIFFRACTION100
5.52-6.950.20153870.17966912X-RAY DIFFRACTION100
6.95-49.240.18843550.15896916X-RAY DIFFRACTION99.53
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)
10.7699023108790.6447518552460.02701277150073.92765848975-0.0706277064583.19212481153-0.02075561673050.150284338490.075589466266-0.337557544996-0.006604016227570.5598620868360.000209466934995-0.7101957523850.02427102233770.338556891380.051330055769-0.06346895644680.481916202913-0.01503027992120.389152205208-9.68921165727238.22894509326.7172945231
22.465730166050.4571377052430.1590504023251.868304153660.3009180320921.513590001960.0137532784093-0.1956269259930.1577404986480.188357577084-0.07248909134240.35656450198-0.178665324448-0.4450078074360.06229545287060.3679191395570.08481587177170.09126451900280.411585950869-0.001285828039250.304652671693-3.67774272677243.36696450243.9167011775
32.29421297566-0.9775942068271.258409872913.40333269989-0.2046822353534.15336003978-0.111884867704-0.1015689481410.2921134823470.4930257033760.113833092577-0.9156597171140.06363881519760.547978882881-0.002863482820890.3733785282660.0450851012031-0.1068295740950.420104854463-0.03330322999040.52038535508431.5268915818245.02435630162.4765443203
44.571296777630.1201828791560.7239646393755.86775578742-1.054187346064.469365010640.03468897325080.3100590724520.12447891225-0.4092084746350.184668321844-1.17313602372-0.4976687160180.618153799636-0.1639721842060.506871041601-0.08018603061130.1270408585610.385629057969-0.1082091877420.50290244479729.448704824251.24893371322.5114105819
50.178620064154-0.46928006680.1064709806131.38329999768-0.6898671117042.012588786380.0403725064738-0.2346661460780.146283046991-0.183376803062-0.120918809745-0.267782076912-0.1563230994810.1670296736050.07420282670180.442187761918-0.01619886135090.08803335684610.305116517519-0.01006239886420.38635600245921.3635965402251.31655192532.7701483518
63.14054337397-0.4680766256460.1966201398053.524840489850.2533941991693.700287043920.008300445416030.4644670292940.322611325059-0.492467002220.110070856122-0.544544340172-0.4169208607230.192327777707-0.09292374111010.629675868489-0.05394592268890.1326208232050.321373524638-0.03468649391960.42403560078822.7262353689251.64747638418.5203585153
72.741374715530.8810155069260.3585237449922.50678473201-0.02059980802792.01782742876-0.04459213457160.635651806512-0.226395167571-0.7873320768860.254584531712-0.829757640995-0.1835622506750.370677094025-0.2139797544570.663657518258-0.001820775096670.217052213030.475244397253-0.1112774707430.5153880505623.3632874184240.20556499110.1656167398
83.390220018522.134440516530.7909847860384.875112600760.8588562726941.375429618350.457394977286-0.132310878218-0.5344500857260.239931232514-0.0650716002589-0.9694548733010.1986474295790.262895744781-0.3433355025270.478244346790.0571481415978-0.08099076232470.358930138695-0.03365593863110.53854559407819.112734004223.29910809722.6174416286
91.37006514809-0.431645547830.04707770801427.801051912450.05996620727631.394075092730.106362438707-0.07216258058830.000197821660645-0.00610900763056-0.0963074817645-0.5972554056460.06578634211090.0854290110255-0.01290791921590.34141066425-0.0181717417817-0.07191574054970.311482605073-0.01141396030090.3328151793746.30670014799210.39545915717.2529392295
102.507746696170.1355885663770.8821248345485.08202493283-0.3985265134184.994164186580.158525010676-0.396767226174-0.3259573033230.598891556457-0.01395576701060.3584981810820.440860300618-0.408604391167-0.143884918020.44206352091-0.0142201233716-0.02774153028870.3867190085580.05085314209320.4872242732251.61318524496198.04235529920.6039824016
113.442980951431.007843123910.4048167202844.09548420924-1.082283473564.113314385470.126569773719-0.170466665623-0.0440038045636-0.1474461995650.05428024812680.7979836717030.0278994080234-0.816905747194-0.1618140359680.513918615881-0.000869628952634-0.1359002590550.4536021767050.009969892065930.584253097498-5.22214663453201.451222778.22947173483
121.538166899330.0381325859924-0.3439834095162.08835519358-0.7908890871642.2425795859-0.0598341187961-0.0430399860178-0.0907981274962-0.0763343598426-0.249828825137-0.5953273860820.1402065753880.5725715442940.2900134701770.3168531604050.04158762071180.002827223366220.4154095889970.07823286016190.43047164618143.926295167278.56756415537.9421567634
131.54375879111-0.527919397253-1.40458260892.853142172950.1770842749384.01674157127-0.0595943059619-0.113832522537-0.1063785751020.346162016529-0.03376446304010.499283431705-0.0154063819623-0.4431963148880.06645393246170.35623369390.01609501210340.047854314190.439703147495-0.0178454474210.3886923044366.73272479388274.75980381963.5997840292
144.45171206873-1.08305079455-1.26043380674.757594792310.06643983840254.54346415833-0.08319139340710.393783561779-0.300302878489-0.4943170589180.1544080954040.5295381727850.429425423128-0.611207604922-0.01228087039530.425107188018-0.0836226410911-0.04572090833610.3580280775020.03500431407630.3080885784727.7109468895270.29550370223.8296442241
151.67056316954-1.19457801441-0.1986097959650.936054540635-0.1520558246661.35850701103-0.220304581122-0.0260500230468-0.0444548011281-0.2606913952330.0599059465298-0.135759330482-0.02698193108820.06749937567870.1316801467680.420954672738-0.0350584629280.04543793376150.298932223042-0.02073415867610.41419349785516.3602932581269.4831760833.419404816
161.627563978230.61443570502-0.2673806272712.36535641894-0.5705840436371.8387061011-0.2236867939270.4234392386280.0292828008977-0.7564707192240.1944199997270.3466867546720.213032710958-0.2860941867080.009783986536540.634784420306-0.0271529811643-0.1146071733320.4409101769670.003951790656480.35541616989813.6494018613279.89742640813.7127695374
173.669444833051.67051108783-4.14520479922.93016177008-1.382971004984.631064762580.378115313387-0.1528284952210.2045984525680.35754628228-0.05583110363990.484637583561-0.42577240632-0.335683891082-0.2071020970290.5609498278980.0267942494599-0.01833419171520.4495764474230.05358386805310.42290547297611.946539732291.08820035529.6975642013
181.889882085810.0857792051156-0.9260074192453.65525787038-1.002569544272.156400464110.2163638099-0.2024122689670.288100262590.137343329708-0.114472095718-0.128399863984-0.4056919242410.334363214382-0.08622993486790.415909563878-0.06303982098160.004206353220130.332349484477-0.00408281535050.27466153622730.7889551169312.26010513520.4489297143
192.053317928440.492230189421-1.027603960533.2741213274-1.657950762234.362909901570.38949058606-0.4517127747180.3730451190310.457366567898-0.260068983877-0.439716392384-0.6816947764981.11579373197-0.1468874313420.66012281477-0.2182541972110.02368018024850.569350472628-0.02885589220910.50732882700137.8105528354323.01932778219.8498737498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 289 )
3X-RAY DIFFRACTION3chain 'A' and (resid 290 through 493 )
4X-RAY DIFFRACTION4chain 'B' and (resid 47 through 83 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 111 )
6X-RAY DIFFRACTION6chain 'B' and (resid 112 through 139 )
7X-RAY DIFFRACTION7chain 'B' and (resid 140 through 250 )
8X-RAY DIFFRACTION8chain 'B' and (resid 251 through 301 )
9X-RAY DIFFRACTION9chain 'B' and (resid 302 through 336 )
10X-RAY DIFFRACTION10chain 'B' and (resid 337 through 430 )
11X-RAY DIFFRACTION11chain 'B' and (resid 431 through 490 )
12X-RAY DIFFRACTION12chain 'C' and (resid 47 through 289 )
13X-RAY DIFFRACTION13chain 'C' and (resid 290 through 493 )
14X-RAY DIFFRACTION14chain 'D' and (resid 47 through 83 )
15X-RAY DIFFRACTION15chain 'D' and (resid 84 through 111 )
16X-RAY DIFFRACTION16chain 'D' and (resid 112 through 250 )
17X-RAY DIFFRACTION17chain 'D' and (resid 251 through 272 )
18X-RAY DIFFRACTION18chain 'D' and (resid 273 through 374 )
19X-RAY DIFFRACTION19chain 'D' and (resid 375 through 485 )

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