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- PDB-5yq5: Crystal structure of human osteomodulin -

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Basic information

Entry
Database: PDB / ID: 5yq5
TitleCrystal structure of human osteomodulin
ComponentsOsteomodulin
KeywordsPROTEIN FIBRIL / collagen / fibril formation / regulation
Function / homology
Function and homology information


Defective CHST6 causes MCDC1 / Defective ST3GAL3 causes MCT12 and EIEE15 / keratan sulfate catabolic process / keratan sulfate biosynthetic process / Keratan sulfate degradation / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Keratan sulfate biosynthesis / regulation of bone mineralization / lysosomal lumen / Golgi lumen ...Defective CHST6 causes MCDC1 / Defective ST3GAL3 causes MCT12 and EIEE15 / keratan sulfate catabolic process / keratan sulfate biosynthetic process / Keratan sulfate degradation / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Keratan sulfate biosynthesis / regulation of bone mineralization / lysosomal lumen / Golgi lumen / collagen-containing extracellular matrix / cell adhesion / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Osteomodulin / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Osteomodulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsCaaveiro, J.M.M. / Tashima, T. / Tsumoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS16H02420 Japan
JSPS15K06962 Japan
CitationJournal: Commun Biol / Year: 2018
Title: Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin.
Authors: Tashima, T. / Nagatoishi, S. / Caaveiro, J.M.M. / Nakakido, M. / Sagara, H. / Kusano-Arai, O. / Iwanari, H. / Mimuro, H. / Hamakubo, T. / Ohnuma, S.I. / Tsumoto, K.
History
DepositionNov 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
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 / _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.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Osteomodulin
B: Osteomodulin
C: Osteomodulin
D: Osteomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,72319
Polymers200,6574
Non-polymers3,06615
Water5,657314
1
A: Osteomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0495
Polymers50,1641
Non-polymers8854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Osteomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9235
Polymers50,1641
Non-polymers7594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Osteomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8284
Polymers50,1641
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Osteomodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9235
Polymers50,1641
Non-polymers7594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.640, 110.700, 122.150
Angle α, β, γ (deg.)90.00, 106.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYAA64 - 36362 - 361
21SERSERGLYGLYBB64 - 36362 - 361
12SERSERGLUGLUAA64 - 36462 - 362
22SERSERGLUGLUCC64 - 36462 - 362
13SERSERGLUGLUAA64 - 36462 - 362
23SERSERGLUGLUDD64 - 36462 - 362
14CYSCYSGLYGLYBB62 - 36360 - 361
24CYSCYSGLYGLYCC62 - 36360 - 361
15GLYGLYGLYGLYBB61 - 36359 - 361
25GLYGLYGLYGLYDD61 - 36359 - 361
16CYSCYSGLUGLUCC62 - 36460 - 362
26CYSCYSGLUGLUDD62 - 36460 - 362

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Osteomodulin / / Keratan sulfate proteoglycan osteomodulin / KSPG osteomodulin / Osteoadherin / OSAD


Mass: 50164.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OMD, SLRR2C, UNQ190/PRO216 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99983
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 200 mM ammonium phosphate dibasic 24 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→35.19 Å / Num. obs: 101333 / % possible obs: 99.2 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.2
Reflection shellResolution: 2.17→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 14545 / CC1/2: 0.609 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XKU

1xku


Resolution: 2.17→35.19 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.636 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24526 5191 5.1 %RANDOM
Rwork0.2169 ---
obs0.21837 96111 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.762 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å2-0.67 Å2
2--0.76 Å20 Å2
3----1.84 Å2
Refinement stepCycle: 1 / Resolution: 2.17→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9985 0 192 314 10491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910493
X-RAY DIFFRACTIONr_bond_other_d0.0020.029590
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.99714255
X-RAY DIFFRACTIONr_angle_other_deg1.048322512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8151223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.59325.328488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.143151892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3631524
X-RAY DIFFRACTIONr_chiral_restr0.1050.21597
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021903
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_it3.7084.1824874
X-RAY DIFFRACTIONr_mcbond_other3.7064.1814873
X-RAY DIFFRACTIONr_mcangle_it5.3656.2596088
X-RAY DIFFRACTIONr_mcangle_other5.3656.2596089
X-RAY DIFFRACTIONr_scbond_it4.7674.8955619
X-RAY DIFFRACTIONr_scbond_other4.764.8935612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3777.1088151
X-RAY DIFFRACTIONr_long_range_B_refined9.37949.07210999
X-RAY DIFFRACTIONr_long_range_B_other9.38449.05710969
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)
11A192440.09
12B192440.09
21A191520.1
22C191520.1
31A190660.1
32D190660.1
41B194040.09
42C194040.09
51B192600.1
52D192600.1
61C194840.09
62D194840.09
LS refinement shellResolution: 2.166→2.222 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 428 -
Rwork0.329 6901 -
obs--97.18 %

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