[English] 日本語
Yorodumi
- PDB-7snc: Pacifastin related protease inhibitors -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7snc
TitlePacifastin related protease inhibitors
ComponentsProtease inhibitor
KeywordsTOXIN / CDP / Pacifastin / protease inhibitor
Function / homologyProtease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / serine-type endopeptidase inhibitor activity / extracellular region / Protease inhibitor
Function and homology information
Biological speciesSchistocerca gregaria (desert locust)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGewe, M.M. / Strong, R.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Sci Transl Med / Year: 2022
Title: Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager.
Authors: Crook, Z.R. / Girard, E.J. / Sevilla, G.P. / Brusniak, M.Y. / Rupert, P.B. / Friend, D.J. / Gewe, M.M. / Clarke, M. / Lin, I. / Ruff, R. / Pakiam, F. / Phi, T.D. / Bandaranayake, A. / ...Authors: Crook, Z.R. / Girard, E.J. / Sevilla, G.P. / Brusniak, M.Y. / Rupert, P.B. / Friend, D.J. / Gewe, M.M. / Clarke, M. / Lin, I. / Ruff, R. / Pakiam, F. / Phi, T.D. / Bandaranayake, A. / Correnti, C.E. / Mhyre, A.J. / Nairn, N.W. / Strong, R.K. / Olson, J.M.
#1: Journal: Nat Struct Mol Biol / Year: 2018
Title: Screening, large-scale production and structure-based classification of cystine-dense peptides
Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S. ...Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S.M. / May, D. / Watson, A. / Chan, M.K. / Bahl, C.D. / Olson, J.M. / Strong, R.K.
History
DepositionOct 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease inhibitor


Theoretical massNumber of molelcules
Total (without water)3,8791
Polymers3,8791
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.761, 80.885, 28.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein/peptide Protease inhibitor


Mass: 3879.375 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistocerca gregaria (desert locust) / Gene: pp-4a / Production host: Homo sapiens (human) / References: UniProt: Q4GZT5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-Sodium tartrate, 20 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 2269 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Χ2: 1.237 / Net I/σ(I): 19.7 / Num. measured all: 14904
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.145.10.0781020.9930.040.0881.37492.7
2.14-2.186.20.0751160.9940.0330.0821.21198.3
2.18-2.226.60.0731140.9980.030.0791.211100
2.22-2.266.80.0741040.9970.030.081.389100
2.26-2.316.80.0661070.9970.0280.0721.265100
2.31-2.376.80.0651180.9940.0270.0711.246100
2.37-2.426.80.0611040.9980.0240.0661.412100
2.42-2.496.70.0621080.9960.0260.0671.109100
2.49-2.566.90.0551140.9980.0220.0591.28100
2.56-2.656.70.0521140.9970.0210.0561.115100
2.65-2.746.80.0471100.9990.0190.0511.296100
2.74-2.856.80.0451180.9980.0190.0491.296100
2.85-2.986.80.0421050.9980.0170.0451.296100
2.98-3.146.70.0391130.9970.0170.0431.194100
3.14-3.336.80.0361120.9990.0150.0391.115100
3.33-3.596.80.0341220.9990.0140.0371.115100
3.59-3.956.60.0331160.9990.0140.0361.207100
3.95-4.526.60.0311140.9940.0140.0341.037100
4.52-5.76.40.0291250.9990.0120.0311.197100
5.7-405.60.0331330.9990.0150.0361.45798.5

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GL1

1gl1


Resolution: 2.5→23.21 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.403 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.649 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 53 3.9 %RANDOM
Rwork0.2092 ---
obs0.2119 1307 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.44 Å2 / Biso mean: 22.268 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 2.5→23.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms264 0 0 16 280
Biso mean---19.4 -
Num. residues----38
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013271
X-RAY DIFFRACTIONr_bond_other_d0.0010.018226
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.687367
X-RAY DIFFRACTIONr_angle_other_deg1.3311.579528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.663537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.17916.15413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4781538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.357154
X-RAY DIFFRACTIONr_chiral_restr0.0790.237
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0263
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree1.433 5 -
Rwork0.337 100 -
all-105 -
obs--100 %

+
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://pdbjlvh1.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