[English] 日本語
Yorodumi
- PDB-3fzz: Structure of GrC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fzz
TitleStructure of GrC
ComponentsGranzyme C
KeywordsHYDROLASE / Cytolysis / Protease / Serine protease / Zymogen
Function / homology
Function and homology information


cytolytic granule / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / killing of cells of another organism / serine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsBuckle, A.M. / Kaiserman, D. / Whisstock, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of granzyme C reveals an unusual mechanism of protease autoinhibition
Authors: Kaiserman, D. / Buckle, A.M. / Van Damme, P. / Irving, J.A. / Law, R.H.P. / Matthews, A.Y. / Bashtannyk-Puhalovich, T. / Langendorf, C. / Thompson, P. / Vandekerckhove, J. / Gevaert, K. / ...Authors: Kaiserman, D. / Buckle, A.M. / Van Damme, P. / Irving, J.A. / Law, R.H.P. / Matthews, A.Y. / Bashtannyk-Puhalovich, T. / Langendorf, C. / Thompson, P. / Vandekerckhove, J. / Gevaert, K. / Whisstock, J.C. / Bird, P.I.
History
DepositionJan 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Granzyme C
B: Granzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0579
Polymers50,3842
Non-polymers6727
Water48627
1
A: Granzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4804
Polymers25,1921
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Granzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5765
Polymers25,1921
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.488, 71.488, 206.696
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHEAA21 - 401 - 20
21ILEILEPHEPHEBB21 - 401 - 20
12GLYGLYLYSLYSAA45 - 24625 - 226
22GLYGLYLYSLYSBB45 - 24625 - 226

-
Components

#1: Protein Granzyme C / Cytotoxic cell protease 2 / CCP2 / B10


Mass: 25192.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Pichia pastoris (fungus)
References: UniProt: P08882, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN IS BASED ON REFERENCE 3 OF UNIPROTKB/SWISS-PROT P08882 (GRAC_MOUSE).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.35 % / Mosaicity: 0.62 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.2M ammonium sulfate, 0.25g/ml PEG 3350, 0.1M sodium cacodylate. Crystals were grown by mixing 2 micro-l of reservoir solution with 2 micro-l of protein solution (20mg/ml in 50mM HEPES pH 6. ...Details: 0.2M ammonium sulfate, 0.25g/ml PEG 3350, 0.1M sodium cacodylate. Crystals were grown by mixing 2 micro-l of reservoir solution with 2 micro-l of protein solution (20mg/ml in 50mM HEPES pH 6.8, 200mM NaCl), VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2005
RadiationMonochromator: OSMIC mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→61.911 Å / Num. obs: 20641 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.484

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.67 Å
Translation2.5 Å39.67 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A1U

1a1u


Resolution: 2.5→39.67 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.797 / SU B: 23.342 / SU ML: 0.228 / SU R Cruickshank DPI: 0.426 / SU Rfree: 0.275 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.42 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1015 4.9 %RANDOM
Rwork0.215 ---
obs0.217 20595 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 102.41 Å2 / Biso mean: 52.157 Å2 / Biso min: 23.85 Å2
Baniso -1Baniso -2Baniso -3
1-4.73 Å22.36 Å20 Å2
2--4.73 Å20 Å2
3----7.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 35 27 3436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223484
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9614744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09223.577137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03115527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7871520
X-RAY DIFFRACTIONr_chiral_restr0.1320.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212646
X-RAY DIFFRACTIONr_mcbond_it1.3432258
X-RAY DIFFRACTIONr_mcangle_it2.40453608
X-RAY DIFFRACTIONr_scbond_it4.21371226
X-RAY DIFFRACTIONr_scangle_it5.934101136
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1647 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.020.05
TIGHT THERMAL0.050.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 66 -
Rwork0.355 1460 -
all-1526 -
obs--99.61 %
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)
13.1428-0.05970.27813.39831.23278.7032-0.0475-0.0623-0.09140.1752-0.0140.00450.49680.38680.0616-0.19170.04110.0483-0.1735-0.0742-0.02829.219-19.897-6.833
23.2495-0.535-1.25733.65680.05178.97510.03980.0376-0.0348-0.115-0.1020.0103-0.5375-0.21410.0623-0.15530.02610.059-0.2505-0.0901-0.023623.125-43.974-27.567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 247
2X-RAY DIFFRACTION2B21 - 247

+
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