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- PDB-4bt9: CRYSTAL STRUCTURE OF THE PEPTIDE(PRO-PRO-GLY)3 BOUND COMPLEX OF N... -

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Entry
Database: PDB / ID: 4bt9
TitleCRYSTAL STRUCTURE OF THE PEPTIDE(PRO-PRO-GLY)3 BOUND COMPLEX OF N- TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-238) TYPE I FROM HUMAN
Components
  • (PRO-PRO-GLY)3 PEPTIDE
  • PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1Procollagen-proline dioxygenase
KeywordsOXIDOREDUCTASE / TETRATRICOPEPTIDE REPEAT MOTIF / COILED-COIL / PROLINE RICH PEPTIDE
Function / homology
Function and homology information


procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase complex / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / L-ascorbic acid binding / collagen fibril organization / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum ...procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase complex / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / L-ascorbic acid binding / collagen fibril organization / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum / mitochondrion / membrane / identical protein binding
Similarity search - Function
Helix Hairpins - #1460 / 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. ...Helix Hairpins - #1460 / 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 / Helix Hairpins / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Prolyl 4-hydroxylase subunit alpha-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAnantharajan, J. / Koski, M.K. / Wierenga, R.K.
CitationJournal: Structure / Year: 2013
Title: The Structural Motifs for Substrate Binding and Dimerization of the Alpha Subunit of Collagen Prolyl 4-Hydroxylase
Authors: Anantharajan, J. / Koski, M.K. / Kursula, P. / Hieta, R. / Bergmann, U. / Myllyharju, J. / Wierenga, R.K.
History
DepositionJun 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Jan 25, 2017Group: Data collection
Revision 1.5Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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-1
B: PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
C: (PRO-PRO-GLY)3 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)55,8103
Polymers55,8103
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-76.4 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.280, 100.930, 68.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1 / Procollagen-proline dioxygenase / 4-PH ALPHA-1 / PROCOLLAGEN-PROLINE\ / 2-OXOGLUTARATE-4-DIOXYGENASE SUBUNIT ALPHA-1 / PROLYL-4 ...4-PH ALPHA-1 / PROCOLLAGEN-PROLINE\ / 2-OXOGLUTARATE-4-DIOXYGENASE SUBUNIT ALPHA-1 / PROLYL-4 HYDROXYLASE TYPE I


Mass: 27519.084 Da / Num. of mol.: 2 / Fragment: COLLAGEN BINDING DOMAIN, RESIDUES 18-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P13674, procollagen-proline 4-dioxygenase
#2: Protein/peptide (PRO-PRO-GLY)3 PEPTIDE


Mass: 771.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.7 % / Description: NONE
Crystal growpH: 6
Details: 10% PEGMME 5000, 10% DMSO, 6% MPD, 0.1 M MES, PH 6.0, 5MM SPERMINE HCL, 5MM (PRO-PRO-GLY)3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.0, 1.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.91
ReflectionResolution: 1.9→40 Å / Num. obs: 40153 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 19.5 % / Biso Wilson estimate: 34.76 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YQ8

2yq8


Resolution: 1.9→58.765 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 1997 5 %
Rwork0.1738 --
obs0.1762 40148 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→58.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 0 281 4173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073994
X-RAY DIFFRACTIONf_angle_d0.9315406
X-RAY DIFFRACTIONf_dihedral_angle_d13.471510
X-RAY DIFFRACTIONf_chiral_restr0.061598
X-RAY DIFFRACTIONf_plane_restr0.004697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.28041460.2452682X-RAY DIFFRACTION100
1.9475-2.00020.28671320.20852684X-RAY DIFFRACTION100
2.0002-2.0590.2741410.18832687X-RAY DIFFRACTION100
2.059-2.12550.25731410.17822710X-RAY DIFFRACTION100
2.1255-2.20150.1891410.16762675X-RAY DIFFRACTION100
2.2015-2.28960.2171400.17652678X-RAY DIFFRACTION100
2.2896-2.39380.17521430.16542715X-RAY DIFFRACTION100
2.3938-2.520.21511410.16472683X-RAY DIFFRACTION100
2.52-2.67790.23571420.16662731X-RAY DIFFRACTION100
2.6779-2.88470.24531440.17082723X-RAY DIFFRACTION100
2.8847-3.17490.24161420.18162718X-RAY DIFFRACTION100
3.1749-3.63430.22311440.16822777X-RAY DIFFRACTION100
3.6343-4.57860.19461460.15622781X-RAY DIFFRACTION100
4.5786-58.79320.22041540.18162907X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.111-0.0439-1.05410.08580.00070.52240.0242-0.1122-0.30230.0347-0.0671-0.00210.05930.04060.03830.1821-0.0147-0.00040.11820.00350.187367.048810.680540.5033
21.3523-0.3364-0.6240.78270.70732.3062-0.0410.1338-0.1095-0.04750.0227-0.12880.28010.20960.00410.19170.03960.01210.15490.02470.200596.93059.985719.0708
30.1048-0.25030.31522.4637-2.09293.13440.02110.37640.003-0.29130.15040.18340.1723-0.6364-0.08380.1747-0.00570.03160.3887-0.01350.206386.109211.5307-2.3638
44.0152-0.2595-1.04850.44110.11380.8695-0.1765-0.156-0.23210.02460.0931-0.03110.15490.01380.06750.1976-0.0139-0.01020.0712-0.01710.174365.84728.161233.4259
52.7401-0.031-0.90410.89410.27741.81580.04510.1990.06980.0148-0.0366-0.0060.04610.03720.00880.16180.020.00020.11250.01350.124787.785412.853824.2171
64.2897-1.6151-0.16362.80630.65151.96870.16980.245-0.1390.1069-0.14890.27650.0404-0.1178-0.02570.1644-0.02930.02110.0932-0.00950.145452.572921.238934.7068
73.40871.898-1.20642.4722-1.06853.12550.1694-0.30110.7351-0.04370.14730.2713-0.5543-0.2464-0.01610.22980.00570.06230.1784-0.11030.229839.059119.126755.5914
81.54750.06441.20111.96020.30331.4750.1585-0.2435-0.4598-0.14420.08460.03860.05720.1922-0.18290.2442-0.0253-0.00340.27490.02150.195242.0383.43257.2163
9-0.5545-0.09410.90271.01331.8293.0617-0.06540.06980.07520.23960.0240.00690.38420.01390.04510.2441-0.07660.02720.4288-0.05270.187451.84517.443873.0231
104.5465-0.18451.43714.74760.41084.4065-0.46160.13010.2089-0.36960.41221.1994-0.00680.0211-0.02460.3337-0.0313-0.01770.52070.00490.379284.000822.6734-8.2432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3 THROUGH 90 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 91 THROUGH 146 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 147 THROUGH 238 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 0 THROUGH 61 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 62 THROUGH 90 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 91 THROUGH 106 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 107 THROUGH 123 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 124 THROUGH 146 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 147 THROUGH 237 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 1 THROUGH 9 )

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