[English] 日本語
Yorodumi
- PDB-4tx4: Crystal Structure of a Single-Domain Cysteine Protease Inhibitor ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tx4
TitleCrystal Structure of a Single-Domain Cysteine Protease Inhibitor from Cowpea (Vigna unguiculata)
ComponentsCysteine proteinase inhibitor
KeywordsHYDROLASE INHIBITOR / Cysteine Protease Inhibitor
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity
Similarity search - Function
Aspartic acid proteinase inhibitor / Cystatin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Cysteine proteinase inhibitor
Similarity search - Component
Biological speciesVigna unguiculata (cowpea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsPereira, H.M. / Valadares, N. / Monteiro-Junior, J.E. / Carvalho, C.P.S. / Grangeiro, T.B.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: Expression in Escherichia coli of cysteine protease inhibitors from cowpea (Vigna unguiculata): The crystal structure of a single-domain cystatin gives insights on its thermal and pH stability.
Authors: Monteiro Junior, J.E. / Valadares, N.F. / Pereira, H.D. / Dyszy, F.H. / da Costa Filho, A.J. / Uchoa, A.F. / de Oliveira, A.S. / da Silveira Carvalho, C.P. / Grangeiro, T.B.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Cysteine proteinase inhibitor
A: Cysteine proteinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9273
Polymers18,8312
Non-polymers961
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-39 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.830, 64.640, 87.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cysteine proteinase inhibitor / / Cystatin


Mass: 9415.605 Da / Num. of mol.: 2 / Fragment: UNP residues 15-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna unguiculata (cowpea) / Plasmid: pET302 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress (DE3) / References: UniProt: Q06445
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 200mM ammonium sulphate, 20% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 17, 2011
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 17850 / Num. obs: 17574 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.81 % / Rmerge F obs: 0.104 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.064 / Χ2: 0.939 / Net I/σ(I): 16.79 / Num. measured all: 66981
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-2.073.470.4570.353.429487283127340.40796.6
2.07-2.210.2610.2315.7210224265926540.26599.8
2.21-2.390.1910.1618.169548246524630.18599.9
2.39-2.610.1330.11311.458949230222980.1399.8
2.61-2.920.0810.07117.388114208220810.081100
2.92-3.360.0470.04625.67115185418460.05399.6
3.36-4.10.0280.03136.566062159515730.03598.6
4.1-5.740.020.02543.434792127112200.02896
5.740.020.02442.8326907917050.02889.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
d*TREKdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→27.339 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 879 5 %
Rwork0.173 16694 -
obs0.1742 17573 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.98 Å2 / Biso mean: 29.735 Å2 / Biso min: 13.02 Å2
Refinement stepCycle: final / Resolution: 1.95→27.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 5 157 1460
Biso mean--37.65 41.76 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141327
X-RAY DIFFRACTIONf_angle_d1.3221788
X-RAY DIFFRACTIONf_chiral_restr0.079193
X-RAY DIFFRACTIONf_plane_restr0.007229
X-RAY DIFFRACTIONf_dihedral_angle_d15.566486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9503-2.07240.23111410.20052676281797
2.0724-2.23230.22251460.174327742920100
2.2323-2.45690.25421470.172127932940100
2.4569-2.81210.18771470.17628002947100
2.8121-3.54170.19571480.173628192967100
3.5417-27.34160.16881500.16582832298295
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)
13.0059-0.3350.39772.9489-1.20326.727-0.3674-0.22590.40790.46590.3067-0.017-0.3296-0.1281-0.00260.20310.0442-0.02410.2086-0.06050.2479-6.0525-6.204716.4632
21.23981.0504-0.52521.72690.20660.43090.0039-0.0297-0.29990.16360.1006-0.13070.03810.1501-0.02710.1762-0.0027-0.0040.2093-0.0490.2037-1.5492-11.183818.8491
31.80870.0385-1.22511.26330.43283.4025-0.0426-0.15080.1561-0.03180.00440.0436-0.3733-0.29730.01010.1390.0456-0.03350.1718-0.04650.201518.6114-1.1948.9981
43.49580.71770.39872.68010.59353.9535-0.1363-0.3804-0.01020.0369-0.0392-0.14030.0772-0.27980.10710.17860.0405-0.00640.1792-0.00970.195223.0412-5.79947.1615
51.98390.2393-2.40910.6465-0.66793.90120.3004-0.16160.6708-0.1166-0.01060.1778-0.55090.0419-0.20870.2603-0.0116-0.01420.207-0.06590.259420.24164.630513.1645
61.40230.7560.20923.21221.20011.6581-0.0070.1069-0.13390.11130.2053-0.09820.06840.06370.03420.13210.0125-0.01310.1605-0.03210.1581-0.9821-9.94817.5735
71.1590.96690.52097.2353.14113.2279-0.0968-0.0823-0.0056-0.25810.3474-0.207-0.17390.14680.02560.15720.0063-0.00970.2058-0.00410.17230.0287-10.269113.6957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 16 through 34 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 35 through 53 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 54 through 94 )B0
4X-RAY DIFFRACTION4chain 'A' and (resid 15 through 39 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 53 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 54 through 81 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 82 through 97 )A0

+
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