[English] 日本語
Yorodumi
- PDB-3mnc: Investigation of global and local effects of radiation damage on ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mnc
TitleInvestigation of global and local effects of radiation damage on porcine pancreatic elastase. Second stage of radiation damage
ComponentsChymotrypsin-like elastase family member 1
KeywordsHYDROLASE / radiation damage / disulfide bridge / atomic resolution
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine 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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.119 Å
AuthorsPetrova, T. / Ginell, S. / Kim, Y. / Joachimiak, G. / Joachimiak, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: X-ray-induced deterioration of disulfide bridges at atomic resolution.
Authors: Petrova, T. / Ginell, S. / Mitschler, A. / Kim, Y. / Lunin, V.Y. / Joachimiak, G. / Cousido-Siah, A. / Hazemann, I. / Podjarny, A. / Lazarski, K. / Joachimiak, A.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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-like elastase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1434
Polymers25,9281
Non-polymers2153
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.139, 57.723, 74.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Chymotrypsin-like elastase family member 1 / Elastase-1


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: The initial concentration of the protein was 10 mg/ml in water. The reservoir contained 25 mM Na2SO4. The cryo-solution contained 25 mM Na2SO4 and 25% glycerol, pH 8.2, VAPOR DIFFUSION, ...Details: The initial concentration of the protein was 10 mg/ml in water. The reservoir contained 25 mM Na2SO4. The cryo-solution contained 25 mM Na2SO4 and 25% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2008
Details: 1.02-M flat mirror made of zerodur providing vertical focusing and rejection of harmonic contamination
RadiationMonochromator: double crystal monochromator utilizing a SI-111 and sagital horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 80647 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 10.65 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.63
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.01 / Num. unique all: 3405 / % possible all: 82.4

-
Processing

Software
NameClassification
HKL-3000data collection
AMoREphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GVK

1gvk


Resolution: 1.119→9.819 Å / Isotropic thermal model: Anisotropic / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1411 3858 -Random
Rwork0.116 ---
obs0.1172 77321 92.21 %-
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2624 Å2-0 Å2-0 Å2
2---0.3379 Å2-0 Å2
3----0.5992 Å2
Refine analyzeLuzzati coordinate error obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.119→9.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 536 2369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_deg1.5
X-RAY DIFFRACTIONf_dihedral_angle_d18.161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.1187-1.13230.231800.2138X-RAY DIFFRACTION180664
1.1323-1.14660.2172990.1881X-RAY DIFFRACTION212775
1.1466-1.16170.17371030.1631X-RAY DIFFRACTION221479
1.1617-1.17760.1831380.1537X-RAY DIFFRACTION236284
1.1776-1.19430.14261190.1366X-RAY DIFFRACTION249788
1.1943-1.21210.15881410.1218X-RAY DIFFRACTION254791
1.2121-1.2310.13021410.1108X-RAY DIFFRACTION261093
1.231-1.25120.14081210.0999X-RAY DIFFRACTION268494
1.2512-1.27270.13611370.0965X-RAY DIFFRACTION267795
1.2727-1.29580.12181570.0942X-RAY DIFFRACTION267296
1.2958-1.32070.13091530.0936X-RAY DIFFRACTION271696
1.3207-1.34760.13491400.0869X-RAY DIFFRACTION270897
1.3476-1.37680.10991340.0837X-RAY DIFFRACTION272896
1.3768-1.40870.1041620.0843X-RAY DIFFRACTION275097
1.4087-1.44390.13131390.0832X-RAY DIFFRACTION275797
1.4439-1.48280.11831290.0809X-RAY DIFFRACTION275797
1.4828-1.52620.11431540.0784X-RAY DIFFRACTION277397
1.5262-1.57530.11291500.0856X-RAY DIFFRACTION275298
1.5753-1.63140.11091340.0832X-RAY DIFFRACTION279398
1.6314-1.69640.11391400.0896X-RAY DIFFRACTION282898
1.6964-1.77320.12741500.095X-RAY DIFFRACTION279999
1.7732-1.8660.11221680.0979X-RAY DIFFRACTION281799
1.866-1.98210.12771450.0984X-RAY DIFFRACTION283399
1.9821-2.13360.12571620.105X-RAY DIFFRACTION2859100
2.1336-2.34570.12831640.1067X-RAY DIFFRACTION283999
2.3457-2.67910.15471520.1159X-RAY DIFFRACTION287999
2.6791-3.35290.12871360.119X-RAY DIFFRACTION277894
3.3529-9.8190.20621100.187X-RAY DIFFRACTION190163

+
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