[English] 日本語
Yorodumi
- PDB-2jet: Crystal structure of a trypsin-like mutant (S189D , A226G) chymot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jet
TitleCrystal structure of a trypsin-like mutant (S189D , A226G) chymotrypsin.
Components
  • CHYMOTRYPSINOGEN B CHAIN A
  • CHYMOTRYPSINOGEN B CHAIN B
  • CHYMOTRYPSINOGEN B CHAIN C
KeywordsHYDROLASE / SUBSTRATE SPECIFICITY / ZYMOGEN / PROTEASE / DIGESTION / SERINE PROTEASE / PROTEIN ENGINEERING
Function / homology
Function and homology information


Activation of Matrix Metalloproteinases / chymotrypsin / response to food / digestion / serine-type peptidase activity / response to nutrient / response to cytokine / protein catabolic process / response to peptide hormone / response to toxic substance ...Activation of Matrix Metalloproteinases / chymotrypsin / response to food / digestion / serine-type peptidase activity / response to nutrient / response to cytokine / protein catabolic process / response to peptide hormone / response to toxic substance / peptidase activity / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJelinek, B. / Katona, G. / Fodor, K. / Venekei, I. / Graf, L.
CitationJournal: Protein J. / Year: 2008
Title: The Crystal Structure of a Trypsin-Like Mutant Chymotrypsin: The Role of Position 226 in the Activity and Specificity of S189D Chymotrypsin.
Authors: Jelinek, B. / Katona, G. / Fodor, K. / Venekei, I. / Graf, L.
History
DepositionJan 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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 "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" 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: CHYMOTRYPSINOGEN B CHAIN A
B: CHYMOTRYPSINOGEN B CHAIN B
C: CHYMOTRYPSINOGEN B CHAIN C


Theoretical massNumber of molelcules
Total (without water)25,6793
Polymers25,6793
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-65.2 kcal/mol
Surface area11930 Å2
MethodPQS
Unit cell
Length a, b, c (Å)34.690, 64.351, 44.224
Angle α, β, γ (deg.)90.00, 102.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide CHYMOTRYPSINOGEN B CHAIN A


Mass: 1544.833 Da / Num. of mol.: 1 / Fragment: RESIDES 19-28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: PANCREAS / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P07338, chymotrypsin
#2: Protein CHYMOTRYPSINOGEN B CHAIN B


Mass: 13880.524 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: PANCREAS / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P07338, chymotrypsin
#3: Protein CHYMOTRYPSINOGEN B CHAIN C


Mass: 10253.702 Da / Num. of mol.: 1 / Fragment: RESIDUES 165-263 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: PANCREAS / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P07338, chymotrypsin
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN C, SER 207 TO ASP ENGINEERED RESIDUE IN CHAIN C, ALA 244 TO GLY
Sequence detailsFIRST FIVE RESIDUE ARE DUE TO THE EXPRESSION CONSTRUCT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.8 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: VAPOR DIFFUSION METHOD, 0.1M HEPES, PH 7.0, 30% PEG6000 AND PROTEIN (15 MG/ML) WITH BENZAMIDINE TWOFOLD EXCESS MIXED 1:1, 20 C

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2005 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→64.42 Å / Num. obs: 9753 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KDQ

1kdq


Resolution: 2.2→43.23 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.834 / SU B: 24.796 / SU ML: 0.332 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDECHAINS WITH 0 OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.334 461 4.8 %RANDOM
Rwork0.276 ---
obs0.279 9145 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.43 Å2
2---0.32 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 0 67 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221720
X-RAY DIFFRACTIONr_bond_other_d0.0010.021113
X-RAY DIFFRACTIONr_angle_refined_deg0.8241.9452352
X-RAY DIFFRACTIONr_angle_other_deg1.1073.0072738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.575226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62226.49157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6915262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.371151
X-RAY DIFFRACTIONr_chiral_restr0.1140.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.021906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
X-RAY DIFFRACTIONr_nbd_refined0.1450.2338
X-RAY DIFFRACTIONr_nbd_other0.1550.21186
X-RAY DIFFRACTIONr_nbtor_refined0.1560.2873
X-RAY DIFFRACTIONr_nbtor_other0.0780.2879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.070.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0740.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1280.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0190.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0411.51438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.04821836
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.073690
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1134.5516
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 40
Rwork0.316 609
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)
19.9548-0.97390.91176.43230.7933.78-0.0034-0.3368-0.23290.0238-0.049-0.1806-0.1871-0.06480.0524-0.195-0.01990.0039-0.24470.0211-0.2791-0.43382.3539.587
29.8726-1.1751-0.06294.9087-0.21696.1232-0.2624-1.8387-1.2740.22910.2344-0.37620.42780.28830.028-0.11010.0054-0.01970.1720.3554-0.02935.0433-5.242420.3145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B19 - 146
2X-RAY DIFFRACTION1A-1 - 10
3X-RAY DIFFRACTION1C151 - 157
4X-RAY DIFFRACTION2C158 - 246

+
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