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

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Basic information

Entry
Database: PDB / ID: 4bta
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 1-244) TYPE I FROM HUMAN
Components
  • PROLINE RICH PEPTIDE
  • PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
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 / collagen fibril organization / L-ascorbic acid binding / 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 / collagen fibril organization / L-ascorbic acid binding / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum / mitochondrion / identical protein binding / membrane
Similarity search - Function
Helix Hairpins - #1460 / 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 ...Helix Hairpins - #1460 / 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 / Helix Hairpins / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Helix non-globular / Special / 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-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsAnantharajan, J. / Koski, M.K. / Pekkala, M. / 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 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 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: PROLINE RICH PEPTIDE


Theoretical massNumber of molelcules
Total (without water)58,8153
Polymers58,8153
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-66.5 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.660, 47.850, 60.290
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 / 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: 29021.723 Da / Num. of mol.: 2 / Fragment: COLLAGEN BINDING DOMAIN, RESIDUES 18-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P13674, procollagen-proline 4-dioxygenase
#2: Protein/peptide PROLINE RICH PEPTIDE / 9 RESIDUE PEPTIDE- PPGPPGPRPG


Mass: 771.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)

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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: 2.11 Å3/Da / Density % sol: 41.66 % / Description: NONE
Crystal growpH: 6
Details: 10% PEGMME5000, 10% DMSO, 10% MPD, 0.1 M MES, PH 6.0, 5MM (PRO-PRO-GLY)3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.8999
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8999 Å / Relative weight: 1
ReflectionResolution: 2.95→33.6 Å / Num. obs: 14997 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.01 % / Biso Wilson estimate: 66.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.01
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.33 / % possible all: 99.1

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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: 2.95→33.8 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 30.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 748 5 %
Rwork0.2269 --
obs0.2296 14988 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.4 Å2
Refinement stepCycle: LAST / Resolution: 2.95→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 0 0 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123760
X-RAY DIFFRACTIONf_angle_d1.7985079
X-RAY DIFFRACTIONf_dihedral_angle_d14.6211416
X-RAY DIFFRACTIONf_chiral_restr0.09567
X-RAY DIFFRACTIONf_plane_restr0.011650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9501-3.17770.33081470.24932808X-RAY DIFFRACTION100
3.1777-3.49720.33981450.2492760X-RAY DIFFRACTION99
3.4972-4.00260.25871490.2152833X-RAY DIFFRACTION100
4.0026-5.04010.22991490.20472841X-RAY DIFFRACTION100
5.0401-33.80240.29541580.23662998X-RAY DIFFRACTION99
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)
17.96436.59122.21046.1631.03090.76220.82950.07110.16362.1086-0.47761.56260.27970.0832-0.23110.716-0.15640.25760.8097-0.1151.077737.1582-1.8464-16.9978
25.07072.20040.18941.509-1.69815.35030.48290.6814-0.99240.1770.3132-0.23891.0574-0.8308-0.70870.7857-0.08930.03890.9067-0.20492.137517.3065-23.4207-21.5531
36.49722.2315-4.71489.1536-4.94424.7190.2171-0.45450.14030.1899-0.47590.1434-0.256-0.01040.24310.6777-0.1-0.07290.5191-0.19470.596449.941219.039-25.3674
44.6022-0.97751.72825.3151-2.32514.8303-0.19440.6039-0.57510.52120.1337-0.50870.4322-0.4331-0.010.65960.0179-0.01240.6626-0.12940.412550.750718.2754-39.948
54.4584-0.87182.34985.0122-3.86083.3613-0.14350.9277-0.3139-1.62760.14910.12550.27070.0025-0.0371.2223-0.0575-0.08740.9905-0.11210.565647.339521.4955-55.9871
65.20512.21051.16074.94430.57342.00950.05791.3086-1.01330.03510.36780.56670.36980.38-0.4220.67270.01610.12210.8169-0.32051.329534.7699-7.4768-24.8413
74.49035.33131.1476.2156-1.60910.9270.10710.9933-0.7697-0.52680.64780.8269-0.0165-0.294-0.47670.5816-0.03480.15770.8107-0.24221.906224.1346-7.0082-23.7452
84.1687-1.957-4.73787.53654.79946.7314-0.3707-1.31110.58021.3011.3050.11541.88580.7881-1.03721.51640.1517-0.73881.45150.45842.39859.4642-34.3275-7.7291
94.24353.0746-2.54773.13990.53467.93870.9979-2.0726-0.72590.8605-0.56950.77651.1311.8023-0.65851.23560.0649-0.12451.96440.44891.878514.5652-32.6509-1.9448
104.0579-4.147-4.82564.94013.80947.40261.2051-0.02061.2686-1.9740.647-1.8663-0.1-0.9594-1.58051.24830.0745-0.18692.1520.66152.3377.9124-28.52135.607
119.5288-7.0253-1.46185.6672.18192.7181-0.8123-0.6997-1.73820.00881.76362.73442.4437-1.3361-0.7761.9353-0.3198-0.25382.74920.16261.929212.9043-30.63112.7661
128.4965.1088-0.92399.5096-0.07821.65991.034-1.90321.37190.3662-1.6277-0.6082-0.39820.08970.14571.9579-0.4045-0.56042.15690.0161.70656.9408-23.510815.7205
133.49462.81150.19985.89120.55020.0530.44290.81341.0675-1.61371.18742.04010.18610.7685-1.1981.41030.1324-0.05332.2338-0.05370.916539.505526.873-54.9199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3 THROUGH 53 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 54 THROUGH 90 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 91 THROUGH 146 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 147 THROUGH 186 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 187 THROUGH 239 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 7 THROUGH 61 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 62 THROUGH 123 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 124 THROUGH 162 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 163 THROUGH 186 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 187 THROUGH 204 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 205 THROUGH 217 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 218 THROUGH 234 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 1 THROUGH 9 )

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