[English] 日本語
Yorodumi
- PDB-4btb: CRYSTAL STRUCTURE OF THE PEPTIDE(PRO)9 BOUND COMPLEX OF N-TERMINA... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more