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- PDB-5kf4: Crystal structure of FN3 domain (Residues P368-P466) of Human col... -

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Basic information

Entry
Database: PDB / ID: 5kf4
TitleCrystal structure of FN3 domain (Residues P368-P466) of Human collagen XX
ComponentsCollagen alpha-1(XX) chain
KeywordsCONTRACTILE PROTEIN / FN3 domain / Human collagen
Function / homology
Function and homology information


Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / collagen trimer / collagen-containing extracellular matrix / endoplasmic reticulum lumen / extracellular region
Similarity search - Function
: / : / Thrombospondin N-terminal -like domains. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily ...: / : / Thrombospondin N-terminal -like domains. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen alpha-1(XX) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsXie, Y. / Cheng, Z. / Zhao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81473114 China
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of the second fibronectin type III (FN3) domain from human collagen alpha 1 type XX
Authors: Zhao, J. / Ren, J. / Wang, N. / Cheng, Z. / Yang, R. / Lin, G. / Guo, Y. / Cai, D. / Xie, Y. / Zhao, X.
#1: Journal: Protein Engineering, Design & Selection / Year: 2012
Title: Design of novel FN3 domains with high stability by a consensus sequence approach
Authors: Jacobs, S.A. / Diem, M.D. / Luo, J. / Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. / ONeil, K.T.
History
DepositionJun 12, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Collagen alpha-1(XX) chain
B: Collagen alpha-1(XX) chain
C: Collagen alpha-1(XX) chain
D: Collagen alpha-1(XX) chain


Theoretical massNumber of molelcules
Total (without water)41,9924
Polymers41,9924
Non-polymers00
Water1,22568
1
A: Collagen alpha-1(XX) chain


Theoretical massNumber of molelcules
Total (without water)10,4981
Polymers10,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagen alpha-1(XX) chain


Theoretical massNumber of molelcules
Total (without water)10,4981
Polymers10,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Collagen alpha-1(XX) chain


Theoretical massNumber of molelcules
Total (without water)10,4981
Polymers10,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Collagen alpha-1(XX) chain


Theoretical massNumber of molelcules
Total (without water)10,4981
Polymers10,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.476, 78.597, 81.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROPROPROchain AAA368 - 4662 - 100
2PROPROPROPROchain BBB368 - 4662 - 100
3ALAALATHRTHRchain CCC369 - 4643 - 98
4ALAALAALAALAchain DDD369 - 4653 - 99

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Components

#1: Protein
Collagen alpha-1(XX) chain


Mass: 10497.936 Da / Num. of mol.: 4 / Fragment: UNP residues 368-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: In vitro translation / Gene: COL20A1, KIAA1510 / Plasmid: pCR2.1 TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P218
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80mM Magnesium Acetate, 50mM Sodium Cacodylate (pH6.5), 30%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2015
RadiationMonochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.5 Å / Num. obs: 14950 / % possible obs: 98.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 22
Reflection shellResolution: 2.5→2.62 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 12 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TES

3tes


Resolution: 2.5→45.864 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 4.45 / Phase error: 26.3
RfactorNum. reflection% reflection
Rfree0.2837 596 4.91 %
Rwork0.2576 --
obs0.2587 12128 92.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.91 Å2 / Biso mean: 32.7632 Å2 / Biso min: 3.84 Å2
Refinement stepCycle: final / Resolution: 2.5→45.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 0 68 2985
Biso mean---26.77 -
Num. residues----391
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1755X-RAY DIFFRACTION14.671TORSIONAL
12B1755X-RAY DIFFRACTION14.671TORSIONAL
13C1755X-RAY DIFFRACTION14.671TORSIONAL
14D1755X-RAY DIFFRACTION14.671TORSIONAL

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