[English] 日本語
Yorodumi
- PDB-4aa8: Bovine chymosin at 1.8A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aa8
TitleBovine chymosin at 1.8A resolution
ComponentsCHYMOSIN
KeywordsHYDROLASE / ASPARTIC PEPTIDASE / RENNET
Function / homology
Function and homology information


chymosin / digestion / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsLangholm Jensen, J. / Molgaard, A. / Navarro Poulsen, J.C. / van den Brink, J.M. / Harboe, M. / Simonsen, J.B. / Qvist, K.B. / Larsen, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Camel and Bovine Chymosin: The Relationship between Their Structures and Cheese-Making Properties.
Authors: Langholm Jensen, J. / Molgaard, A. / Navarro Poulsen, J.C. / Harboe, M.K. / Simonsen, J.B. / Lorentzen, A.M. / Hjerno, K. / van den Brink, J.M. / Qvist, K.B. / Larsen, S.
History
DepositionNov 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.page_last / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHYMOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9569
Polymers35,6731
Non-polymers2848
Water6,666370
1
A: CHYMOSIN
hetero molecules

A: CHYMOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,91318
Polymers71,3452
Non-polymers56716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2180 Å2
ΔGint-129.9 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.610, 79.170, 113.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1328-

CL

21A-2368-

HOH

-
Components

#1: Protein CHYMOSIN / PREPRORENNIN


Mass: 35672.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: MUCOSA / Organ: ABOMASUM / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: P00794, chymosin
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR: 1.5 M NACL, 100 MM NAH2PO4, PH 5.5. SAMPLE: 30 MG/ML PROTEIN IN 50 MM NAH2PO4, PH 6.0.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Feb 19, 2009
Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M).
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 30113 / % possible obs: 99.7 % / Observed criterion σ(I): 4.8 / Redundancy: 8.1 % / Biso Wilson estimate: 17.86 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.8 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CMS

1cms


Resolution: 1.801→26.554 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 22.56 / Stereochemistry target values: ML
Details: DISORDERED LOOPS 159-162, 242-245, 278-282, AND 291-292 WERE MODELLED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.2147 1520 5.1 %
Rwork0.177 --
obs0.1789 30027 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.149 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.5055 Å20 Å20 Å2
2---4.2078 Å20 Å2
3----8.2976 Å2
Refinement stepCycle: LAST / Resolution: 1.801→26.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 8 370 2889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082577
X-RAY DIFFRACTIONf_angle_d1.0323508
X-RAY DIFFRACTIONf_dihedral_angle_d14.043908
X-RAY DIFFRACTIONf_chiral_restr0.076386
X-RAY DIFFRACTIONf_plane_restr0.005458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8011-1.85920.26941360.22962533X-RAY DIFFRACTION99
1.8592-1.92570.24911290.21142550X-RAY DIFFRACTION100
1.9257-2.00270.24491450.18172567X-RAY DIFFRACTION100
2.0027-2.09380.21281310.18322594X-RAY DIFFRACTION100
2.0938-2.20420.23491420.17442520X-RAY DIFFRACTION99
2.2042-2.34220.22871390.17572587X-RAY DIFFRACTION100
2.3422-2.52290.23281430.18562579X-RAY DIFFRACTION100
2.5229-2.77660.26181330.1912609X-RAY DIFFRACTION100
2.7766-3.17780.24261370.18212598X-RAY DIFFRACTION100
3.1778-4.00150.16461460.1572629X-RAY DIFFRACTION100
4.0015-26.55690.18191390.1652741X-RAY DIFFRACTION99

+
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