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- PDB-5mx0: Crystal structure of human fibromodulin -

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Basic information

Entry
Database: PDB / ID: 5mx0
TitleCrystal structure of human fibromodulin
ComponentsFibromodulin
KeywordsSTRUCTURAL PROTEIN / Leucine-rich repeat / extracellular matrix / collagen binding
Function / homology
Function and homology information


Defective CHST6 causes MCDC1 / Defective ST3GAL3 causes MCT12 and EIEE15 / transforming growth factor beta receptor complex assembly / keratan sulfate catabolic process / keratan sulfate biosynthetic process / Keratan sulfate degradation / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Keratan sulfate biosynthesis / collagen fibril organization / ECM proteoglycans ...Defective CHST6 causes MCDC1 / Defective ST3GAL3 causes MCT12 and EIEE15 / transforming growth factor beta receptor complex assembly / keratan sulfate catabolic process / keratan sulfate biosynthetic process / Keratan sulfate degradation / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Keratan sulfate biosynthesis / collagen fibril organization / ECM proteoglycans / lysosomal lumen / extracellular matrix / Golgi lumen / collagen-containing extracellular matrix / extracellular space / extracellular region
Similarity search - Function
Fibromodulin / Leucine rich repeat N-terminal domain / 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
NICKEL (II) ION / Fibromodulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsParacuellos, P. / Hohenester, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101748/Z/13/Z United Kingdom
CitationJournal: Matrix Biol. / Year: 2017
Title: Structural and functional analysis of two small leucine-rich repeat proteoglycans, fibromodulin and chondroadherin.
Authors: Paracuellos, P. / Kalamajski, S. / Bonna, A. / Bihan, D. / Farndale, R.W. / Hohenester, E.
History
DepositionJan 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_special_symmetry / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _pdbx_struct_special_symmetry.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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Fibromodulin
B: Fibromodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,66914
Polymers81,6192
Non-polymers6,05012
Water10,196566
1
A: Fibromodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8357
Polymers40,8101
Non-polymers3,0256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibromodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8357
Polymers40,8101
Non-polymers3,0256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.110, 98.930, 111.340
Angle α, β, γ (deg.)90.00, 107.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-874-

HOH

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Components

#1: Protein Fibromodulin / FM / Collagen-binding 59 kDa protein / Keratan sulfate proteoglycan fibromodulin / KSPG fibromodulin


Mass: 40809.684 Da / Num. of mol.: 2
Mutation: Y38S, Y39S, Y42S, Y45S, Y47S, Y50S, Y53S, Y55S, Y63S, Y65S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMOD, FM, SLRR2E / Plasmid: pCEP-Pu / Cell line (production host): HEK293 c18 / Production host: Homo sapiens (human) / References: UniProt: Q06828
#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml protein + 26% (w/v) PEG 3350, 200 mM lithium sulphate monohydrate, 100 mM Tris-HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.21→65.913 Å / Num. obs: 55434 / % possible obs: 99 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.046 / Net I/σ(I): 9.5
Reflection shellResolution: 2.21→2.27 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.84 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.523 / Rpim(I) all: 0.737 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XKU

1xku


Resolution: 2.21→65.913 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 2823 5.1 %
Rwork0.1793 --
obs0.1812 55367 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→65.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4881 0 396 566 5843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035416
X-RAY DIFFRACTIONf_angle_d0.7597408
X-RAY DIFFRACTIONf_dihedral_angle_d11.4972108
X-RAY DIFFRACTIONf_chiral_restr0.03890
X-RAY DIFFRACTIONf_plane_restr0.003909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.24810.3181310.29722609X-RAY DIFFRACTION99
2.2481-2.2890.35111300.32542661X-RAY DIFFRACTION99
2.289-2.3330.33111370.28952553X-RAY DIFFRACTION99
2.333-2.38070.32481310.28932621X-RAY DIFFRACTION98
2.3807-2.43240.34121560.27662591X-RAY DIFFRACTION98
2.4324-2.4890.29781280.25992629X-RAY DIFFRACTION100
2.489-2.55130.2671520.24632638X-RAY DIFFRACTION100
2.5513-2.62020.27111520.22782643X-RAY DIFFRACTION100
2.6202-2.69730.25251240.22192640X-RAY DIFFRACTION100
2.6973-2.78440.30251450.2232631X-RAY DIFFRACTION100
2.7844-2.88390.26691540.21542589X-RAY DIFFRACTION99
2.8839-2.99940.26361340.22322635X-RAY DIFFRACTION98
2.9994-3.13590.2751330.22692579X-RAY DIFFRACTION97
3.1359-3.30120.25971350.21792675X-RAY DIFFRACTION99
3.3012-3.5080.20861570.18442641X-RAY DIFFRACTION100
3.508-3.77890.17631330.15612634X-RAY DIFFRACTION99
3.7789-4.15910.17461510.12412653X-RAY DIFFRACTION99
4.1591-4.76080.14491290.11242586X-RAY DIFFRACTION97
4.7608-5.99750.17351430.12922678X-RAY DIFFRACTION99
5.9975-65.94210.18751680.16412658X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -41.2711 Å / Origin y: 19.1171 Å / Origin z: 132.5475 Å
111213212223313233
T0.3546 Å20.0076 Å2-0.036 Å2-0.3001 Å2-0.009 Å2--0.3275 Å2
L0.7149 °20.0881 °2-0.3375 °2-0.3527 °2-0.0733 °2--0.6785 °2
S0.1025 Å °-0.0115 Å °-0.0163 Å °0.009 Å °-0.0378 Å °-0.0048 Å °0.0363 Å °0.0005 Å °0.0077 Å °
Refinement TLS groupSelection details: all

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