[English] 日本語
Yorodumi
- PDB-1c3l: SUBTILISIN-CARLSBERG COMPLEXED WITH XENON (8 BAR) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c3l
TitleSUBTILISIN-CARLSBERG COMPLEXED WITH XENON (8 BAR)
ComponentsSUBTILISIN-CARLSBERG
KeywordsHYDROLASE / XENON / SERINE-PROTEINASE
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / XENON / Subtilisin Carlsberg
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.16 Å
AuthorsPrange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S.
Citation
Journal: Proteins / Year: 1998
Title: Exploring hydrophobic sites in proteins with xenon or krypton.
Authors: Prange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R.
#1: Journal: J.Appl.Crystallogr. / Year: 1994
Title: On the Preparation and X-ray Data Collection of Isomorphous Xenon Derivatives
Authors: Schiltz, M. / Prange, T. / Fourme, R.
#2: Journal: Structure / Year: 1995
Title: The Catalytic Site of Serine-Proteinases as a Specific Binding Cavity for Xenon
Authors: Schiltz, M. / Fourme, R. / Broutin, I. / Prange, T.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: The Structure of Subtilopeptidase 1. X-ray Crystallographic Data
Authors: Petsko, G.A. / Tsernoglou, D.
History
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SUBTILISIN-CARLSBERG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6297
Polymers27,2791
Non-polymers3506
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.500, 55.300, 53.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingmonoclinic
Space group name H-MP212121

-
Components

#1: Protein SUBTILISIN-CARLSBERG


Mass: 27279.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 5.5
Details: protein: 15mg/ml in acetate buffer (0.05M) plus sodium azide (10-5M). Sodium formate as the crystallizing agent(4M). Crystals as elongated needles in two weeks., pH 5.50, MICRODIALYSIS, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: unknown / Details: Shotton, D.M., (1968) J.Mol.Biol., 32, 155.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %solution of elastase11
20.01 Msodium acetate11
30.02 Msodium sulfate11

-
Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.961
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961 Å / Relative weight: 1
ReflectionResolution: 2.16→15 Å / Num. all: 44356 / Num. obs: 40233 / % possible obs: 0.83 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11
Reflection shellResolution: 2.16→2.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.167 / Num. unique all: 1172 / % possible all: 65

-
Processing

Software
NameVersionClassification
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementStarting model: 1SCA

1sca


Resolution: 2.16→7 Å / Num. parameters: 8135 / Num. restraintsaints: 7863 / σ(F): 3 / σ(I): 4 / Stereochemistry target values: Engh & Huber / Details: 8135 parameters refined using 7863 restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1010 -random
Rwork0.151 ---
all0.1624 11117 --
obs0.151 9455 85 %-
Refinement stepCycle: LAST / Resolution: 2.16→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 3 117 2038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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