[English] 日本語
Yorodumi
- PDB-1gpp: Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gpp
TitleCrystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I
ComponentsENDONUCLEASE PI-SCEI
KeywordsENDONUCLEASE / HOMING / PROTEIN SPLICING
Function / homology
Function and homology information


Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / protein metabolic process / intein-mediated protein splicing ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / protein metabolic process / intein-mediated protein splicing / intron homing / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / H+-transporting two-sector ATPase / proton transmembrane transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / Golgi membrane / mRNA binding / DNA binding / ATP binding
Similarity search - Function
Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region ...Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
V-type proton ATPase catalytic subunit A
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWerner, E. / Wende, W. / Pingoud, A. / Heinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: High Resolution Crystal Structure of Domain I of the Saccharomyces Cerevisiae Homing Endonuclease Pi-Scei
Authors: Werner, E. / Wende, W. / Pingoud, A. / Heinemann, U.
History
DepositionNov 7, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDONUCLEASE PI-SCEI


Theoretical massNumber of molelcules
Total (without water)27,0351
Polymers27,0351
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.856, 47.595, 60.297
Angle α, β, γ (deg.)90.00, 121.41, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein ENDONUCLEASE PI-SCEI / HOMING ENDONUCLEASE PI-SCEI / VMA1-DERIVED ENDONUCLEASE


Mass: 27034.643 Da / Num. of mol.: 1
Fragment: PROTEIN SPLICING DOMAIN, RESIDUES 284-466,693-736, SEE REMARK 999
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GLY183 LINKS ILE182 AND ALA410, WHERE IN THE FULL LENGTH PROTEIN IS DOMAIN II
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P17255, H+-transporting two-sector ATPase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMUTATIONS: ARG327SER, VAL350MET, ILE415VAL, LEU466GLY
Sequence detailsTHE PROTEIN PI-SCEI IS AN INTEIN OF THE PRIMARY TRANSLATION PRODUCT OF THE ATP SYNTHASE (SWS ENTRY ...THE PROTEIN PI-SCEI IS AN INTEIN OF THE PRIMARY TRANSLATION PRODUCT OF THE ATP SYNTHASE (SWS ENTRY P17255). IT SPLICES ITSELF OUT OF THE PRECURSOR. PI-SCEI IS A TWO-DOMAIN PROTEIN. THE ENTRY 1GPP REPRESENTS DOMAIN I WHICH CONSISTS OF RESIDUES 1 TO 182 AND 410 TO 453, DOMAIN II IN THE FULL LENGTH PROTEIN CONSISTS OF RESIDUES 183 TO 409. GLU183 WAS ENGINEERD AS LINKER BETWEEN THE TWO PARTS OF THE DOMAIN. THE MUTATIONS R54S, M67V AND I132V ARE NOT ENGINEERED BUT TURNED OUT TO BE PRESENT AFTER CLONING FROM BAKERS YEAST COMMERCIALLY AVAILABLE FOR US. THE SEQADV ONLY SHOWS THE DIFFERENCE TO THE DATABASE ENTRY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 4.8
Details: 30 % PEG4000, 0.1 M SODIUM CITRATE PH 5.6, 0.2 M NH4-ACETATE
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.35 mMprotein-RNA1drop
230 %PEG40001reservoir
30.1 Msodium citrate1reservoirpH5.6
40.2 Mammonium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8453
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 1.35→20 Å / Num. obs: 51602 / % possible obs: 94.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 34.5
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 2.5 / % possible all: 64.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 359618
Reflection shell
*PLUS
% possible obs: 64.1 % / Num. unique obs: 1141

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VDE

1vde


Resolution: 1.35→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.249 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FIRST 8 RESIDUES OF THE HIS-TAG AND RESIDUES 55 - 66 ARE NOT VISIBLE IN ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3744 7.3 %RANDOM
Rwork0.15 ---
obs0.153 47840 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å2-0.61 Å2
2--1.92 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 303 2029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211769
X-RAY DIFFRACTIONr_bond_other_d0.0010.021610
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9582391
X-RAY DIFFRACTIONr_angle_other_deg0.95233751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3453216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.115327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1590.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021952
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02363
X-RAY DIFFRACTIONr_nbd_refined0.2620.3318
X-RAY DIFFRACTIONr_nbd_other0.20.31537
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.5275
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0890.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.440.537
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0041.51087
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.97921764
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8383682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7584.5626
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.237 197
Rwork0.176 2498
Refinement
*PLUS
% reflection Rfree: 7 % / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.83

+
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://pdbjlvh1.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