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- PDB-9htd: Peptide-substrate-binding (PSB) domain of human type II collagen ... -

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Basic information

Entry
Database: PDB / ID: 9htd
TitlePeptide-substrate-binding (PSB) domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Hyp-Gly-Pro-Ala-Gly-Pro-Hyp-Gly.
Components
  • GLY-PRO-ALA-GLY-PRO-HYP-GLY
  • Prolyl 4-hydroxylase subunit alpha-2
KeywordsPROTEIN BINDING / collagen / tetratricopeptide / extracellular matrix
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. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
GLYCINE / Prolyl 4-hydroxylase subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsSulu, R. / Rahman, M.M. / Wierenga, R.K. / Koski, M.K.
Funding support Finland, 2items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation220013 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Proteins / Year: 2025
Title: Binding Differences of the Peptide-Substrate-Binding Domain of Collagen Prolyl 4-Hydroxylases I and II for Proline- and Hydroxyproline-Rich Peptides.
Authors: Rahman, M.M. / Sulu, R. / Adediran, B. / Tu, H. / Salo, A.M. / Murthy, S. / Myllyharju, J. / Wierenga, R.K. / Koski, M.K.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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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: GLY-PRO-ALA-GLY-PRO-HYP-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0947
Polymers12,6982
Non-polymers3965
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS experiments show that the PSB-II construct is monomer in the solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-16 kcal/mol
Surface area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.655, 56.655, 68.828
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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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
Details: N-terminal His-tag. Construct including residues Met142-Glu236.
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HA2, UNQ290/PRO330 / Production host: Escherichia coli (E. coli)
References: UniProt: O15460, procollagen-proline 4-dioxygenase
#2: Protein/peptide GLY-PRO-ALA-GLY-PRO-HYP-GLY


Mass: 777.822 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The two first N-terminal residues of the peptide are not modelled and not seen in the electron density.
Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M ammonium sulphate, 10% dioxane, 100 mM MES, 2 mM Pro-Hyp-Gly-Pro-Ala-Gly-Pro-Hyp-Gly.
Temp details: Cold room temperature is fluctuating between 277 and 279.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2018 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→49.06 Å / Num. obs: 12786 / % possible obs: 97.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Net I/σ(I): 14.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.075 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 718 / CC1/2: 0.556 / Rpim(I) all: 0.433 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→49.06 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.21 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1951 687 5.374 %
Rwork0.1648 12096 -
all0.166 --
obs-12783 96.113 %
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: 39.127 Å2
Baniso -1Baniso -2Baniso -3
1--0.196 Å2-0.098 Å2-0 Å2
2---0.196 Å20 Å2
3---0.637 Å2
Refinement stepCycle: LAST / Resolution: 1.751→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 25 55 882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.012838
X-RAY DIFFRACTIONr_bond_other_d0.0020.016760
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.8441130
X-RAY DIFFRACTIONr_angle_other_deg0.7411.7681749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.556599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.49456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33510133
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.0631043
X-RAY DIFFRACTIONr_chiral_restr0.0970.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021000
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02190
X-RAY DIFFRACTIONr_nbd_refined0.2190.2177
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1420.2662
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2415
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.2457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.244
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.213
X-RAY DIFFRACTIONr_nbd_other0.1070.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.211
X-RAY DIFFRACTIONr_mcbond_it4.2463.566414
X-RAY DIFFRACTIONr_mcbond_other4.2013.56413
X-RAY DIFFRACTIONr_mcangle_it5.786.293507
X-RAY DIFFRACTIONr_mcangle_other5.7766.296508
X-RAY DIFFRACTIONr_scbond_it6.0254.133424
X-RAY DIFFRACTIONr_scbond_other5.9534.094420
X-RAY DIFFRACTIONr_scangle_it8.947.317623
X-RAY DIFFRACTIONr_scangle_other8.8947.245618
X-RAY DIFFRACTIONr_lrange_it9.9938.529968
X-RAY DIFFRACTIONr_lrange_other9.73437.843959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.751-1.7960.279490.278885X-RAY DIFFRACTION98.2124
1.796-1.8460.27460.255882X-RAY DIFFRACTION98.4093
1.846-1.8990.255490.262867X-RAY DIFFRACTION97.9679
1.899-1.9570.315300.264829X-RAY DIFFRACTION96.8433
1.957-2.0220.261640.198777X-RAY DIFFRACTION97.4508
2.022-2.0920.213580.19745X-RAY DIFFRACTION96.9807
2.092-2.1710.272400.171760X-RAY DIFFRACTION97.6801
2.171-2.260.172340.161714X-RAY DIFFRACTION96.5161
2.26-2.360.165320.141687X-RAY DIFFRACTION95.9947
2.36-2.4750.154390.147654X-RAY DIFFRACTION96.7877
2.475-2.6080.206340.158627X-RAY DIFFRACTION96.3557
2.608-2.7660.29250.17596X-RAY DIFFRACTION95.8333
2.766-2.9560.154450.165547X-RAY DIFFRACTION95.4839
2.956-3.1920.172250.15517X-RAY DIFFRACTION95.4225
3.192-3.4950.154410.153459X-RAY DIFFRACTION93.985
3.495-3.9060.171200.14435X-RAY DIFFRACTION93.047
3.906-4.5050.162210.135375X-RAY DIFFRACTION92.9577
4.505-5.5060.126130.153335X-RAY DIFFRACTION91.0995
5.506-7.7380.301160.199247X-RAY DIFFRACTION88.8513
7.738-49.060.28460.17158X-RAY DIFFRACTION87.7005

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