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- PDB-6kam: Crystal structure of FKRP in complex with Ba ion, CDP-ribtol, and... -

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Basic information

Entry
Database: PDB / ID: 6kam
TitleCrystal structure of FKRP in complex with Ba ion, CDP-ribtol, and sugar acceptor
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 / basement membrane organization / skeletal muscle fiber differentiation / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to activity / glycolytic process / protein tetramerization / neuron migration / sarcolemma / brain development / protein processing / lipid metabolic process / in utero embryonic development / inflammatory response / response to xenobiotic stimulus / Golgi membrane / Golgi apparatus / extracellular space / nucleoplasm / identical protein binding / metal ion binding / cytosol
Similarity search - Function
LicD family / : / : / LicD family / Fukutin-related protein stem domain
Similarity search - Domain/homology
: / CYTIDINE-5'-DIPHOSPHATE / PHOSPHATE ION / D-ribitol / Ribitol 5-phosphate transferase FKRP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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 2.1Oct 16, 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)205,46430
Polymers200,1074
Non-polymers5,35726
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16500 Å2
ΔGint-99 kcal/mol
Surface area74040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.571, 119.240, 254.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 4 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

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Sugars , 2 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGlcpNAcb1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE
#4: 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 / Feature type: SUBJECT OF INVESTIGATION
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 , 6 types, 211 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-RB0 / D-ribitol


Mass: 152.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H12O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
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: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.46→45.69 Å / Num. obs: 86984 / % possible obs: 99.76 % / Redundancy: 6.5 % / Biso Wilson estimate: 55.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.051 / Rrim(I) all: 0.095 / Net I/σ(I): 19.8
Reflection shellResolution: 2.46→2.51 Å / Rmerge(I) obs: 1.315 / Num. unique obs: 8055 / CC1/2: 0.745 / Rpim(I) all: 0.759 / Rrim(I) all: 1.424

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→45.69 Å / SU ML: 0.3515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2135 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2492 4332 4.98 %
Rwork0.2084 82652 -
obs0.2104 86984 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.35 Å2
Refinement stepCycle: LAST / Resolution: 2.46→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13769 0 290 193 14252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007314498
X-RAY DIFFRACTIONf_angle_d0.948819896
X-RAY DIFFRACTIONf_chiral_restr0.0512222
X-RAY DIFFRACTIONf_plane_restr0.0062601
X-RAY DIFFRACTIONf_dihedral_angle_d7.535910083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.490.36051250.35322608X-RAY DIFFRACTION95.93
2.49-2.520.39061500.36182706X-RAY DIFFRACTION99.93
2.52-2.550.37561360.35542741X-RAY DIFFRACTION99.86
2.55-2.590.36451520.33122706X-RAY DIFFRACTION99.97
2.59-2.620.37971530.33932728X-RAY DIFFRACTION99.9
2.62-2.660.37071410.31992710X-RAY DIFFRACTION99.96
2.66-2.690.39141350.31352747X-RAY DIFFRACTION99.83
2.69-2.730.34121520.29262708X-RAY DIFFRACTION99.83
2.73-2.780.29521420.27562734X-RAY DIFFRACTION99.93
2.78-2.820.30891480.26442723X-RAY DIFFRACTION99.76
2.82-2.870.35931400.26072736X-RAY DIFFRACTION99.97
2.87-2.920.3071450.26192745X-RAY DIFFRACTION99.97
2.92-2.980.29111310.26682729X-RAY DIFFRACTION99.79
2.98-3.040.30471540.26862759X-RAY DIFFRACTION99.93
3.04-3.110.30671480.26432733X-RAY DIFFRACTION100
3.11-3.180.29031450.2512723X-RAY DIFFRACTION99.83
3.18-3.260.31681460.2522748X-RAY DIFFRACTION99.9
3.26-3.350.2841400.23162736X-RAY DIFFRACTION99.83
3.35-3.440.26161550.23042727X-RAY DIFFRACTION99.93
3.44-3.550.26751450.22112775X-RAY DIFFRACTION99.97
3.55-3.680.2491500.2132730X-RAY DIFFRACTION99.93
3.68-3.830.24441400.19482785X-RAY DIFFRACTION99.8
3.83-40.22581510.17752742X-RAY DIFFRACTION99.93
4-4.210.21591420.17562793X-RAY DIFFRACTION99.9
4.21-4.480.21711230.16312816X-RAY DIFFRACTION99.9
4.48-4.820.20051530.15572771X-RAY DIFFRACTION99.97
4.82-5.310.18561330.16232835X-RAY DIFFRACTION99.93
5.31-6.070.22081450.19252821X-RAY DIFFRACTION99.97
6.07-7.650.20711670.1772839X-RAY DIFFRACTION100
7.65-45.690.19171450.16152998X-RAY DIFFRACTION99.43
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)
12.050003112990.9385700332030.1263765290972.658426147720.4707002882243.31022840651-0.0286894503833-0.04473672223420.2094205879260.0171292597956-0.07481136262980.432358743147-0.389085353081-0.5012632671560.1186311829560.6247115148610.140418413922-0.007524526945240.4512873361930.01308969764970.424845203445-8.08811531963243.09898834.9542353443
24.248303780421.094145114412.886516051231.402911352511.467252727482.329105950780.054108268857-0.103248130777-0.1439739675670.4641518530370.0325205675359-0.1946414888680.0222501134586-0.14724123201-0.03997848346260.7273757706750.01931935591960.0005568028829860.4428318799380.05392256955550.36168958260715.3068902174238.21250691751.7127235758
34.92371243679-0.3750149552721.980814976155.668165644771.157393853495.2639650022-0.1644862573580.05482169993210.3786742001230.6715553412140.165556309292-1.07184363216-0.01213845335650.58271722703-0.005769351192120.6949617934380.00569296100061-0.2039457569070.5017848366450.04206713082690.65983066735834.154726354246.33899091864.6087453166
44.477701728551.64940694030.4341285089856.116789020060.7232298231023.30453111606-0.1512010841860.0959559521763-0.0543261004654-0.1398217188710.227861732469-1.18816111631-0.3450557744680.434035686581-0.2148077470790.676040247757-0.0961074187220.04301902224360.439750240581-0.06409035069210.66601985358629.7678269497251.42775873422.4695199879
52.5228415140.9733025083060.6488232181073.022253740360.7959352769552.37429475070.313061993306-0.469965630841-0.124189450621-0.00341117258629-0.372855735898-0.384158467403-0.07073875412330.0905632819264-0.04757200410570.649552856137-0.0579418529325-0.03415723682710.4399375417960.04107794207310.52866148413121.8201329802251.44735022332.8858403467
63.032780793221.035496716520.3238556357033.871762196811.251296902293.52457424361-0.0167750053420.5219384893960.0916035689679-0.8023824035780.276210971645-0.682284818704-0.581422523820.437696591352-0.1128083297640.871766934892-0.1348866654420.1686561061940.468973043885-0.01487692883340.62631615741424.3936068519252.18442412814.3205097979
73.323249454562.13575845530.686311804053.694647048471.214111350072.05551450189-0.05404443866750.53795060879-0.630057719098-0.4220418265890.305903191699-0.795418684567-0.07409735280210.311115099043-0.247676027250.7521368603180.0001919041701130.1204430038710.450733449233-0.09220885332150.62701255872623.5825946913237.96901813111.5688741679
81.476032873882.6460580171.355171108164.830236205322.102398372981.031007509750.565599567861-0.206637956672-0.6036658758130.0901414808086-0.0716033222249-1.59730874707-0.1433235704320.309971147686-0.2907809746180.7428630054410.0213225465667-0.1608563010530.514319799915-0.01591105638790.97068603432220.2446012148223.56278892122.0825726982
92.21959632882-0.2850078654760.2696535438756.070601444070.348193740542.648847736220.137489693174-0.25699951203-0.2625541636650.319746257991-0.0676467631665-0.09633992005850.428021049568-0.256066719426-0.06836370139410.48625157673-0.0445589172546-0.0761672450030.3647316246070.05998846868380.412343076350.177777070526201.99870822516.0602171327
101.917933026140.132426315048-0.4799602934421.78294780421-0.2651004155471.64194419083-0.101335803973-0.227603695715-0.1600888949820.0895750032632-0.115894219833-0.3811878672170.2718219700790.3399276747560.2093366398930.6601332339690.0468605228337-0.06269214699340.4768054445660.06710940334110.50308797652644.6979829783278.66922349237.4404515275
112.82461537327-0.714377992529-2.287439991612.14264392643-0.1424478907795.2226158289-0.007066493391190.03846967622310.01119190970190.32528695103-0.1032358470410.559833685901-0.545234843015-0.6144703856990.1496861846920.7600181844650.05162163243870.07532864516050.496952330967-0.0855534679370.5229009445246.61577438002277.42455810563.1548563404
121.0380734172-0.742863717642-0.6632858264480.928207476321.302688514287.45510776646-0.4344782481080.010104520802-0.7155742346960.129668267592-0.07941369457990.8354430700880.977379529531-0.5220760551880.5456991071050.944802021696-0.0615539794250.1676659760730.665768110512-0.05666690633610.865308637859.24378472573262.88145861563.1507489735
131.866001778290.917479687216-0.1618784403832.79483556391-0.4028200159941.3714060795-0.1150367337990.2552150341670.07818849605-0.4111306322290.1338788139630.3176727230830.00159515497021-0.14827543727-0.01400298568350.683077682082-0.0134608272688-0.0760501242280.404098068268-0.006040432981940.38833153621512.9694368478277.87919907619.6615151234
142.226416411360.729965195283-0.3309913091293.56577786798-1.169204123792.312635050960.335280509268-0.3377226030570.2941149084210.299689915121-0.310934184041-0.182259437934-0.609527506140.489089505082-0.0177587012520.703037529816-0.149297122560.009557788601320.473109735659-0.00899702465650.39869258263335.485481154317.33806056720.0410250465
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 491 )
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 150 )
7X-RAY DIFFRACTION7chain 'B' and (resid 151 through 253 )
8X-RAY DIFFRACTION8chain 'B' and (resid 254 through 296 )
9X-RAY DIFFRACTION9chain 'B' and (resid 297 through 491 )
10X-RAY DIFFRACTION10chain 'C' and (resid 47 through 289 )
11X-RAY DIFFRACTION11chain 'C' and (resid 290 through 454 )
12X-RAY DIFFRACTION12chain 'C' and (resid 455 through 491 )
13X-RAY DIFFRACTION13chain 'D' and (resid 47 through 271 )
14X-RAY DIFFRACTION14chain 'D' and (resid 272 through 491 )

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