[English] 日本語
Yorodumi
- PDB-1czi: CHYMOSIN COMPLEX WITH THE INHIBITOR CP-113972 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1czi
TitleCHYMOSIN COMPLEX WITH THE INHIBITOR CP-113972
Components
  • CHYMOSIN
  • CP-113972 (NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / ASPARTYL PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE / Chymosin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGroves, M.R. / Dhanaraj, V. / Pitts, J.E. / Badasso, M. / Hoover, D. / Nugent, P. / Blundell, T.L.
Citation
Journal: Protein Eng. / Year: 1998
Title: A 2.3 A resolution structure of chymosin complexed with a reduced bond inhibitor shows that the active site beta-hairpin flap is rearranged when compared with the native crystal structure.
Authors: Groves, M.R. / Dhanaraj, V. / Badasso, M. / Nugent, P. / Pitts, J.E. / Hoover, D.J. / Blundell, T.L.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: X-Ray Analyses of Aspartic Proteinases. Iv. Structure and Refinement at 2.2 A Resolution of Bovine Chymosin
Authors: Newman, M. / Safro, M. / Frazao, C. / Khan, G. / Zdanov, A. / Tickle, I.J. / Blundell, T.L. / Andreeva, N.
History
DepositionJan 15, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Aug 9, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_initial_refinement_model / software / struct_conn / struct_ref_seq
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_special_symmetry / pdbx_validate_symm_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: CHYMOSIN
P: CP-113972 (NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE)


Theoretical massNumber of molelcules
Total (without water)36,4032
Polymers36,4032
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.780, 132.780, 81.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11E-527-

HOH

-
Components

#1: Protein CHYMOSIN / RENIN


Mass: 35672.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Description: CALF / Cell: FUNDUS / Organ: STOMACH / Production host: Escherichia coli (E. coli) / References: UniProt: P00794, chymosin
#2: Protein/peptide CP-113972 (NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE) / PFIZER INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 730.697 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.91 Å3/Da / Density % sol: 35.56 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMsodium phosphate1reservoir
31.5 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→21.1 Å / Num. obs: 62777 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 5.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.7 / % possible all: 97.3
Reflection
*PLUS
Num. obs: 12125 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Num. measured all: 62777 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 97.3 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
AGROVATA/ROTAVATA(CCP4 VERSION 2.X)data reduction
AMoREphasing
RESTRAINrefinement
CCP4V 2.X (AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CMS WITHOUT LOOP 71 - 81

4cms


Resolution: 2.3→9.97 Å / σ(F): 0
Details: OTHER REFINEMENT REMARKS: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE ATOM AND HETATM RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE ...Details: OTHER REFINEMENT REMARKS: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE ATOM AND HETATM RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION - B = 8 * (PI)**2 * U**2. DENSITY FOR REGIONS E 156 - E 162 AND E 290 - E 292 IS POOR, AS INDICATED BY HIGHER TEMPERATURE FACTORS FOR THESE REGIONS. THE ELECTRON DENSITY FOR RESIDUES E 240 - E 244 IS NOT CONVINCING. AS A RESULT THIS REGION IS NOT PRECISELY DETERMINED. THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION - B = 8 * (PI)**2 * U**2. DENSITY FOR REGIONS E 156 - E 162 AND E 290 - E 292 IS POOR, AS INDICATED BY HIGHER TEMPERATURE FACTORS FOR THESE REGIONS. THE ELECTRON DENSITY FOR RESIDUES E 240 - E 244 IS NOT CONVINCING. AS A RESULT THIS REGION IS NOT PRECISELY DETERMINED.
RfactorNum. reflection% reflection
Rwork0.1954 --
obs-12125 98 %
Refinement stepCycle: LAST / Resolution: 2.3→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 0 191 2745
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11988 / σ(F): 1 / Rfactor all: 0.19
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