[English] 日本語
Yorodumi
- PDB-1fmz: CRYSTAL STRUCTURE OF A MUTANT WINGED BEAN CHYMOTRYPSIN INHIBITOR ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fmz
TitleCRYSTAL STRUCTURE OF A MUTANT WINGED BEAN CHYMOTRYPSIN INHIBITOR PROTEIN, N14K.
ComponentsCHYMOTRYPSIN INHIBITOR 3
KeywordsHYDROLASE INHIBITOR / Beta Trefoil
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Chymotrypsin inhibitor 3
Similarity search - Component
Biological speciesPsophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsDattagupta, J.K. / Chakrabarti, C. / Ravichandran, S. / Dasgupta, J. / Ghosh, S.
Citation
Journal: PROTEIN ENG. / Year: 2001
Title: The role of Asn14 in the stability and conformation of the reactive-site loop of winged bean chymotrypsin inhibitor: crystal structures of two point mutants Asn14-->Lys and Asn14-->Asp.
Authors: Ravichandran, S. / Dasgupta, J. / Chakrabarti, C. / Ghosh, S. / Singh, M. / Dattagupta, J.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallography of a Kunitz-type Serine Protease Inhibitor: The 90K Structure of Winged bean Chymotrypsin Inhibitor (WCI) at 2.13A resolution.
Authors: Ravichandran, S. / Sen, U. / Chakrabarti, C. / Dattagupta, J.K.
#2: Journal: Proteins / Year: 1999
Title: Refined crystal structure (2.3A) of a double-headed Winged bean alpha-Chymotrypsin Inhibitor and location of its second reactive site
Authors: Dattagupta, J.K. / Podder, A. / Chakrabarti, C. / Sen, U. / Mukhopadhyay, D. / Dutta, S.K. / Singh, M.
#3: Journal: Protein Expr.Purif. / Year: 1997
Title: cDNA cloning, expression and rapid purification of Kunitz-type Winged bean Chymotrypsin Inhibitor
Authors: Ghosh, S. / Singh, M.
History
DepositionAug 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: CHYMOTRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1706
Polymers20,6891
Non-polymers4805
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CHYMOTRYPSIN INHIBITOR 3
hetero molecules

A: CHYMOTRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,33912
Polymers41,3792
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area2950 Å2
ΔGint-161 kcal/mol
Surface area18710 Å2
MethodPISA, PQS
3
A: CHYMOTRYPSIN INHIBITOR 3
hetero molecules

A: CHYMOTRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,33912
Polymers41,3792
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_435x-y-1,-y-2,-z1
Buried area2520 Å2
ΔGint-124 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.86, 60.86, 208.43
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-900-

SO4

21A-400-

HOH

31A-401-

HOH

DetailsThe biological assembly is a monomer

-
Components

#1: Protein CHYMOTRYPSIN INHIBITOR 3 / WCI-3


Mass: 20689.408 Da / Num. of mol.: 1 / Mutation: N14K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean)
Organ: SEED / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P10822
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Ammonium sulfate, Sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: Dattagupta, J.K., (1999) Proteins: Struct., Funct., Genet., 35, 321.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.6 mg/mlprotein1drop
271.4 mMTris-HCl1drop
3286 mM1dropNaCl
41.4 %ammonium sulfate1drop
52.9 mMsodium acetate1drop
625 %ammonium sulfate1reservoir
760 mMsodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→15 Å / Num. all: 147330 / Num. obs: 13051 / % possible obs: 88.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 5.2
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.282 / % possible all: 88.1
Reflection
*PLUS
Num. measured all: 147330
Reflection shell
*PLUS
% possible obs: 91.8 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.05→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used Maximum likelihood target function
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1334 -Random
Rwork0.193 ---
all0.21 147330 --
obs0.21 13051 86.1 %-
Refinement stepCycle: LAST / Resolution: 2.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 25 179 1605
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.21 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d2.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

+
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