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- PDB-4btb: CRYSTAL STRUCTURE OF THE PEPTIDE(PRO)9 BOUND COMPLEX OF N-TERMINA... -

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Basic information

Entry
Database: PDB / ID: 4btb
TitleCRYSTAL STRUCTURE OF THE PEPTIDE(PRO)9 BOUND COMPLEX OF N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-238) TYPE I FROM HUMAN
Components
  • POLY PROLINE 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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 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 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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
C: POLY PROLINE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)28,4112
Polymers28,4112
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-9.4 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.930, 53.043, 79.928
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number5
Space group name H-MC121

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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: 27519.084 Da / Num. of mol.: 1 / Fragment: COLLAGEN BINDING DOMAIN, RESIDUES 18-255
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 POLY PROLINE PEPTIDE


Mass: 892.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.03 Å3/Da / Density % sol: 59.42 % / Description: NONE
Crystal growpH: 9
Details: 20% PEG 6000, 0.1M BICINE 9, 5MM SPERMINE HCL, 5MM (PRO)9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER PLATINIUM-135 / Detector: CCD / Date: Oct 3, 2012 / Details: HELIOS MX MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→43.6 Å / Num. obs: 25406 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 13.26 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.05 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.46 / % possible all: 94

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Processing

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

2yq8


Resolution: 1.899→30.262 Å / SU ML: 0.21 / σ(F): 1.37 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1310 5.2 %
Rwork0.1826 --
obs0.1853 25400 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→30.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 0 218 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072006
X-RAY DIFFRACTIONf_angle_d0.9822724
X-RAY DIFFRACTIONf_dihedral_angle_d13.605765
X-RAY DIFFRACTIONf_chiral_restr0.063302
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8986-1.97470.28061220.25232606X-RAY DIFFRACTION97
1.9747-2.06450.28751450.23012656X-RAY DIFFRACTION100
2.0645-2.17330.24841540.20042657X-RAY DIFFRACTION100
2.1733-2.30940.24531310.19422678X-RAY DIFFRACTION100
2.3094-2.48770.23571490.18832672X-RAY DIFFRACTION100
2.4877-2.73790.24991530.18952687X-RAY DIFFRACTION100
2.7379-3.13370.23211440.19162688X-RAY DIFFRACTION100
3.1337-3.94670.22751470.17282702X-RAY DIFFRACTION100
3.9467-30.26590.21751650.15922744X-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)
10.6867-0.12180.20950.0102-0.38954.405-0.09630.15350.0057-0.0357-0.03860.03810.0073-0.0940.04670.1505-0.01890.00630.12230.01140.129727.182671.269571.2684
22.37610.1351-0.91921.0415-1.88993.5474-0.1182-0.25070.09120.10140.05-0.08940.32570.10430.0430.13630.0658-0.00780.1073-0.01660.14224.613967.803699.287
34.07230.3335-0.76851.12590.71243.1447-0.1760.5616-0.3537-0.1138-0.0031-0.16010.1585-0.1793-0.02850.1458-0.0243-0.04140.1034-0.01650.17139.276765.37951.7721
41.7243-0.4158-2.03830.3620.94313.22210.15311.06421.3272-0.206-0.03290.8564-1.6661-0.6585-0.09640.5380.0644-0.07520.43280.20940.751842.370980.906647.9367
54.4198-1.3053-0.15563.5296-0.42481.38570.00840.09420.25020.24130.0273-0.42990.00980.1383-0.01860.1625-0.075-0.02670.1703-0.02480.275960.031369.910554.9494
65.5306-1.9818-0.91464.19761.21313.191-0.279-0.9860.75890.47240.0261-1.4819-0.11350.545-0.43280.2738-0.0461-0.14210.36390.00960.598774.327163.651461.2114
74.8209-3.30011.7153.9235-0.93698.857-0.05710.2015-0.16740.5208-0.1175-1.12990.12880.92780.18460.24130.0388-0.10670.20470.02250.512572.596857.047156.6597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 54 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 55 THROUGH 90 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 91 THROUGH 132 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 133 THROUGH 146 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 147 THROUGH 217 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 218 THROUGH 236 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 0 THROUGH 8 )

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