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- PDB-6evm: Crystal structure of a Pro-9 complexed peptide-substrate-binding ... -

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Basic information

Entry
Database: PDB / ID: 6evm
TitleCrystal structure of a Pro-9 complexed peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase
Components
  • Pro-9
  • 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 peptide-substrate-binding domain / 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. ...Prolyl 4-hydroxylase alpha-subunit, N-terminal / Prolyl 4-Hydroxylase alpha-subunit, N-terminal region / Prolyl 4-hydroxylase peptide-substrate-binding domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Jan 17, 2024Group: 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
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-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9874
Polymers12,8122
Non-polymers1742
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-10 kcal/mol
Surface area6150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.899, 56.899, 67.871
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-459-

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-9


Mass: 892.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide having 9 proline residues. / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.45 M ammonium sulphate, 10% DMSO, 2.5 mM Pro-9, 4% hexenediol, 100 mM MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Aug 11, 2016 / Details: HELIOS MX MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→39.9 Å / Num. obs: 8956 / % possible obs: 99.4 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.019 / Net I/σ(I): 25.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 384 / Rpim(I) all: 0.21 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XPREPProteum 2 packagedata reduction
SADABSProteum 2 packagedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EVL

6evl


Resolution: 2→39.875 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.53
RfactorNum. reflection% reflection
Rfree0.2191 1677 10.15 %
Rwork0.1696 --
obs0.1746 8927 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 9 106 949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006870
X-RAY DIFFRACTIONf_angle_d0.8911185
X-RAY DIFFRACTIONf_dihedral_angle_d7.159705
X-RAY DIFFRACTIONf_chiral_restr0.039124
X-RAY DIFFRACTIONf_plane_restr0.005158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05740.30161350.23581199X-RAY DIFFRACTION94
2.0574-2.12380.23451380.21391231X-RAY DIFFRACTION100
2.1238-2.19970.22541440.17731269X-RAY DIFFRACTION100
2.1997-2.28770.27251380.26271187X-RAY DIFFRACTION97
2.2877-2.39180.19921440.17081283X-RAY DIFFRACTION100
2.3918-2.51790.18761320.15851206X-RAY DIFFRACTION100
2.5179-2.67560.2321400.16821271X-RAY DIFFRACTION100
2.6756-2.88220.23311400.16351240X-RAY DIFFRACTION100
2.8822-3.17210.22371390.15561281X-RAY DIFFRACTION100
3.1721-3.63090.19281480.15241199X-RAY DIFFRACTION100
3.6309-4.57350.18951300.1361271X-RAY DIFFRACTION100
4.5735-39.8750.22751490.17781205X-RAY DIFFRACTION97

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