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- PDB-9j23: Structure of a triple-helix region of human Collagen type II from... -

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Basic information

Entry
Database: PDB / ID: 9j23
TitleStructure of a triple-helix region of human Collagen type II from Trautec
ComponentsTriple-helix region of human collagen type II
KeywordsSTRUCTURAL PROTEIN / Human collagen II / Triple-helix
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFan, X. / Zhai, Y. / Chu, Y. / Fu, S. / Li, D. / Feng, P. / Cao, K. / Li, J. / Si, Y. / Ma, L. / Qian, S.
Funding support1items
OrganizationGrant numberCountry
Jiangsu Trautec Medical Technology Co.,LtdCQ20230004/CE20235002/CQ20230005
CitationJournal: To Be Published
Title: Structure of a triple-helix region of human Collagen type II from Trautec
Authors: Fan, X. / Zhai, Y. / Chu, Y. / Fu, S. / Li, D. / Feng, P. / Cao, K. / Li, J. / Si, Y. / Ma, L. / Qian, S.
History
DepositionAug 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triple-helix region of human collagen type II
B: Triple-helix region of human collagen type II
C: Triple-helix region of human collagen type II


Theoretical massNumber of molelcules
Total (without water)8,3973
Polymers8,3973
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-23 kcal/mol
Surface area5000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.987, 20.042, 44.985
Angle α, β, γ (deg.)90.000, 99.984, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Triple-helix region of human collagen type II


Mass: 2799.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 33.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Index-G12:0.2M MgCl2, 0.1M HEPES pH7.5, 25% PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.75→44.3 Å / Num. obs: 6457 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.908 / Net I/σ(I): 3.5
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 346 / CC1/2: 0.812

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K6F

1k6f


Resolution: 1.75→44.3 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.293 / SU ML: 0.165 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.165
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2879 299 4.636 %
Rwork0.2407 6151 -
all0.243 --
obs-6450 99.737 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.743 Å2-0 Å20.446 Å2
2--1.249 Å20 Å2
3----2.023 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms554 0 0 84 638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012589
X-RAY DIFFRACTIONr_bond_other_d0.0010.017513
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.807828
X-RAY DIFFRACTIONr_angle_other_deg0.4321.6771245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.711581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.88756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.9921036
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.6451012
X-RAY DIFFRACTIONr_chiral_restr0.0610.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02704
X-RAY DIFFRACTIONr_gen_planes_other00.0288
X-RAY DIFFRACTIONr_nbd_refined0.1830.2200
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.2461
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2314
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.231
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.23
X-RAY DIFFRACTIONr_nbd_other0.1490.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.216
X-RAY DIFFRACTIONr_mcbond_it1.3141.532333
X-RAY DIFFRACTIONr_mcbond_other1.3121.529332
X-RAY DIFFRACTIONr_mcangle_it2.1722.725411
X-RAY DIFFRACTIONr_mcangle_other2.1692.727412
X-RAY DIFFRACTIONr_scbond_it1.6461.832256
X-RAY DIFFRACTIONr_scbond_other1.6431.834257
X-RAY DIFFRACTIONr_scangle_it2.6153.227417
X-RAY DIFFRACTIONr_scangle_other2.6123.228418
X-RAY DIFFRACTIONr_lrange_it4.28720.465693
X-RAY DIFFRACTIONr_lrange_other4.13316.965671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.343190.28445X-RAY DIFFRACTION99.7849
1.795-1.8450.333230.288436X-RAY DIFFRACTION99.3506
1.845-1.8980.341140.251418X-RAY DIFFRACTION100
1.898-1.9560.309290.248417X-RAY DIFFRACTION99.5536
1.956-2.020.323140.246408X-RAY DIFFRACTION100
2.02-2.0910.338180.24376X-RAY DIFFRACTION99.7468
2.091-2.170.408190.239378X-RAY DIFFRACTION100
2.17-2.2580.244140.226371X-RAY DIFFRACTION99.4832
2.258-2.3580.242170.24346X-RAY DIFFRACTION100
2.358-2.4730.332180.256326X-RAY DIFFRACTION99.422
2.473-2.6060.316170.274313X-RAY DIFFRACTION100
2.606-2.7640.407160.223291X-RAY DIFFRACTION99.6753
2.764-2.9540.37140.207294X-RAY DIFFRACTION99.6764
2.954-3.1890.191170.218264X-RAY DIFFRACTION100
3.189-3.4920.228160.224244X-RAY DIFFRACTION99.6169
3.492-3.9010.18110.192219X-RAY DIFFRACTION99.5671
3.901-4.4990.225100.211204X-RAY DIFFRACTION100
4.499-5.4960.38230.267174X-RAY DIFFRACTION100
5.496-7.7130.28880.284138X-RAY DIFFRACTION99.3197
7.713-44.30.08520.44889X-RAY DIFFRACTION98.913

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