[English] 日本語
Yorodumi
- PDB-2bdz: Mexicain from Jacaratia mexicana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bdz
TitleMexicain from Jacaratia mexicana
ComponentsMexicain
KeywordsHYDROLASE / mexicain / Cysteine protease / Peptidase_C1 / papain-like
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / extracellular region
Similarity search - Function
Papain-like cysteine endopeptidase / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A ...Papain-like cysteine endopeptidase / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesJacaratia mexicana (bonete)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsGavira, J.A. / Oliver-Salvador, M.C. / Gonzalez-Ramirez, L.A. / Soriano-Garcia, M. / Garcia-Ruiz, J.M.
Citation
Journal: To be Published
Title: Crystallographic structure of Mexicain from Jacaratia mexicana
Authors: Gavira, J.A. / Oliver-Salvador, M.C. / Gonzalez-Ramirez, L.A. / Soriano-Garcia, M. / Garcia-Ruiz, J.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray analysis of Mexicain
Authors: Oliver-Salvador, M.C. / Gonzalez-Ramirez, L.A. / Gavira, J.A. / Soriano-Garcia, M. / Garcia-Ruiz, J.M.
History
DepositionOct 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 23, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Aminoacids R58 and T70 appear in the deposited sequence P84346 (name: MEX1_JACME) of the ...SEQUENCE Aminoacids R58 and T70 appear in the deposited sequence P84346 (name: MEX1_JACME) of the SWS data base as Y58 and P70 respectively but there are clear evidences for the current substitutions pointing to sequenciation errors.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mexicain
B: Mexicain
C: Mexicain
D: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6178
Polymers95,1754
Non-polymers1,4424
Water6,828379
1
A: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1542
Polymers23,7941
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1542
Polymers23,7941
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1542
Polymers23,7941
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1542
Polymers23,7941
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.356, 90.454, 80.391
Angle α, β, γ (deg.)90.00, 92.636, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is the monomer. The asymetric unit contains four biological units named A,B,C and D.

-
Components

#1: Protein
Mexicain


Mass: 23793.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: latex / Source: (natural) Jacaratia mexicana (bonete)
References: UniProt: P84346, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 20 % (w/v) PEGl 6000, 0.1 M citrate, 15 % (v/v) ethanolamine, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER / Wavelength: 1.5418
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Sep 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40.8 Å / Num. obs: 47249 / % possible obs: 99.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.095 / Χ2: 3.115 / Net I/σ(I): 17.271
Reflection shellResolution: 2.1→2.18 Å / % possible obs: 97.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.495 / Num. measured obs: 4587 / Χ2: 1.694 / % possible all: 97.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0005refinement
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACT1.6data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, ...Starting model: The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, 1gec, 1ppo, 1meg and 1pci

1yal

1gec

1ppo

1meg

1pci


Resolution: 2.1→40.8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.066 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MolProbity, XtalView were also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 4576 10 %RANDOM
Rwork0.177 ---
all0.183 ---
obs-40977 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.046 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.27 Å2
2--1.05 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 100 379 6951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226786
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.969206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38823.958283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.555151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8471536
X-RAY DIFFRACTIONr_chiral_restr0.0690.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025166
X-RAY DIFFRACTIONr_nbd_refined0.2030.23462
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2607
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.218
X-RAY DIFFRACTIONr_mcbond_it1.23524312
X-RAY DIFFRACTIONr_mcangle_it1.81936742
X-RAY DIFFRACTIONr_scbond_it1.322900
X-RAY DIFFRACTIONr_scangle_it1.80132464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.103-2.1580.2972950.1892707350885.576
2.158-2.2170.2633150.1822739341689.403
2.217-2.2810.2642890.1782794335591.893
2.281-2.3520.2573020.1822687320393.319
2.352-2.4290.2613050.1832666314494.497
2.429-2.5140.2682870.1852614303495.616
2.514-2.6090.2492920.1892527293995.917
2.609-2.7150.2752790.1962424279696.674
2.715-2.8360.2322680.1882393272097.831
2.836-2.9740.2562740.1732268258498.375
2.974-3.1340.2272500.182163245098.49
3.134-3.3240.2292350.1732086233699.358
3.324-3.5530.2022120.1711969219699.317
3.553-3.8370.2192000.1571849205599.708
3.837-4.2030.181890.1541681187699.68
4.203-4.6970.2221620.151549171399.883
4.697-5.4210.2261500.1671353150699.801
5.421-6.6310.2391310.2051144127999.687
6.631-9.3460.195950.167909100899.603
9.346-80.3220.3460.27545557686.979

+
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