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- PDB-6evo: Crystal structure the peptide-substrate-binding domain of human t... -

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Basic information

Entry
Database: PDB / ID: 6evo
TitleCrystal structure the peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Arg-Gly-Pro-Pro-Gly.
Components
  • PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY
  • Prolyl 4-hydroxylase subunit alpha-2
KeywordsHYDROLASE / tetratricopeptide repeat / collagen synthesis / prolyl 4-hydroxylase
Function / homology
Function and homology information


procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / L-ascorbic acid binding / electron transfer activity / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum / nucleoplasm / cytosol
Similarity search - Function
Prolyl 4-hydroxylase alpha-subunit, N-terminal / Prolyl 4-Hydroxylase alpha-subunit, N-terminal region / Prolyl 4-hydroxylase / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Tetratricopeptide repeat domain ...Prolyl 4-hydroxylase alpha-subunit, N-terminal / Prolyl 4-Hydroxylase alpha-subunit, N-terminal region / Prolyl 4-hydroxylase / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Prolyl 4-hydroxylase subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsMurthy, A.V. / Sulu, R. / Koski, M.K. / Wierenga, R.K.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: Protein Sci. / Year: 2018
Title: Structural enzymology binding studies of the peptide-substrate-binding domain of human collagen prolyl 4-hydroxylase (type-II): High affinity peptides have a PxGP sequence motif.
Authors: Murthy, A.V. / Sulu, R. / Koski, M.K. / Tu, H. / Anantharajan, J. / Sah-Teli, S.K. / Myllyharju, J. / Wierenga, R.K.
History
DepositionNov 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl 4-hydroxylase subunit alpha-2
C: PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1797
Polymers12,7522
Non-polymers4275
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-18 kcal/mol
Surface area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.382, 55.382, 72.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-473-

HOH

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Components

#1: Protein Prolyl 4-hydroxylase subunit alpha-2 / 4-PH alpha-2 / Procollagen-proline / 2-oxoglutarate-4-dioxygenase subunit alpha-2


Mass: 11920.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HA2, UNQ290/PRO330 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS
References: UniProt: O15460, procollagen-proline 4-dioxygenase
#2: Protein/peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY


Mass: 831.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide, commercial. / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.45 M ammonium sulphate, 10% DMSO, 5 mM PPGPRGPPG, 10 mM EDTA, 100 mM MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2017
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.55→48 Å / Num. obs: 19323 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.02 / Net I/σ(I): 19
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 2 / Num. unique obs: 157 / Rpim(I) all: 0.366 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 1.55→47.962 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.41
RfactorNum. reflection% reflection
Rfree0.1802 1925 10.01 %
Rwork0.1579 --
obs0.1602 19238 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→47.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms829 0 22 82 933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008908
X-RAY DIFFRACTIONf_angle_d0.9511233
X-RAY DIFFRACTIONf_dihedral_angle_d14.863552
X-RAY DIFFRACTIONf_chiral_restr0.049127
X-RAY DIFFRACTIONf_plane_restr0.007162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58880.24771340.23271213X-RAY DIFFRACTION100
1.5888-1.63170.24681370.22031218X-RAY DIFFRACTION100
1.6317-1.67970.24241390.19691220X-RAY DIFFRACTION100
1.6797-1.7340.23611330.19751220X-RAY DIFFRACTION100
1.734-1.79590.24121370.18411236X-RAY DIFFRACTION100
1.7959-1.86780.19471300.18091215X-RAY DIFFRACTION100
1.8678-1.95290.23391350.21091215X-RAY DIFFRACTION98
1.9529-2.05580.18511370.14691215X-RAY DIFFRACTION100
2.0558-2.18460.16361380.1371245X-RAY DIFFRACTION100
2.1846-2.35330.18291390.14861219X-RAY DIFFRACTION99
2.3533-2.59010.15491330.14131233X-RAY DIFFRACTION99
2.5901-2.96490.19091430.14841250X-RAY DIFFRACTION100
2.9649-3.73520.15311410.1471269X-RAY DIFFRACTION100
3.7352-47.98520.17271490.15681345X-RAY DIFFRACTION100

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