[English] 日本語
Yorodumi
- PDB-7a1h: Crystal structure of wild-type CI2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a1h
TitleCrystal structure of wild-type CI2
ComponentsSubtilisin-chymotrypsin inhibitor-2A
KeywordsPROTEIN BINDING / Protease inhibitor
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Subtilisin-chymotrypsin inhibitor-2A
Function and homology information
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsOlsen, J.G. / Teilum, K. / Hamborg, L. / Roche, J.V.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF15OC0016360 Denmark
Citation
Journal: Commun Biol / Year: 2021
Title: Synergistic stabilization of a double mutant in chymotrypsin inhibitor 2 from a library screen in E. coli.
Authors: Hamborg, L. / Granata, D. / Olsen, J.G. / Roche, J.V. / Pedersen, L.E. / Nielsen, A.T. / Lindorff-Larsen, K. / Teilum, K.
#1: Journal: Biorxiv / Year: 2020
Title: Synergistic stabilization of a double mutant in CI2 from an in-cell library screen
Authors: Hamborg, L. / Granata, D. / Olsen, J.G. / Roche, J.V. / Pedersen, L.E. / Nielsen, A.T. / Lindorff-Larsen, K. / Teilum, K.
History
DepositionAug 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Subtilisin-chymotrypsin inhibitor-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5063
Polymers7,3141
Non-polymers1922
Water54030
1
A: Subtilisin-chymotrypsin inhibitor-2A
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)90,06936
Polymers87,76312
Non-polymers2,30624
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation4_575-x,-y+2,z1
crystal symmetry operation5_455y-1,-x+y,z1
crystal symmetry operation6_665x-y+1,x+1,z1
crystal symmetry operation7_467y-1,x+1,-z+21
crystal symmetry operation8_677x-y+1,-y+2,-z+21
crystal symmetry operation9_557-x,-x+y,-z+21
crystal symmetry operation10_667-y+1,-x+1,-z+21
crystal symmetry operation11_457-x+y-1,y,-z+21
crystal symmetry operation12_577x,x-y+2,-z+21
Buried area22740 Å2
ΔGint-419 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.266, 68.266, 52.605
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

-
Components

#1: Protein Subtilisin-chymotrypsin inhibitor-2A / CI-2A


Mass: 7313.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P01053
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.25 %
Description: Beautiful three dimensional crystals with clear hexagonal faces. Size of crystals ranging from a few micrometer to app. 1 mm. Become blue when soaked with "Izit".
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40 % (NH4)2SO4, 50 mM Tris-Hcl, pH 8.0. Protein concentration app 75 mg/mL.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Agilent SuperNova / Wavelength: 1.5406 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: May 9, 2019 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 6063 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→1.949 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 453 / CC1/2: 0.565 / Rpim(I) all: 0.332 / % possible all: 99.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å13.56 Å
Translation1.9 Å13.56 Å

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASER2.5.7phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CI2

2ci2


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.733 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 290 4.8 %RANDOM
Rwork0.2029 ---
obs0.2053 5773 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.81 Å2 / Biso mean: 23.35 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0.37 Å2-0 Å2
2---0.74 Å20 Å2
3---2.41 Å2
Refinement stepCycle: final / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms513 0 10 30 553
Biso mean--50.81 25.98 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02528
X-RAY DIFFRACTIONr_bond_other_d0.0030.02544
X-RAY DIFFRACTIONr_angle_refined_deg2.0732.018716
X-RAY DIFFRACTIONr_angle_other_deg1.02831254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.607563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.04524.76221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32815104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.012154
X-RAY DIFFRACTIONr_chiral_restr0.110.287
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021558
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0298
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 21 -
Rwork0.248 399 -
all-420 -
obs--99.76 %

+
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