[English] 日本語
Yorodumi
- PDB-3pw3: Crystal structure of a cysteine protease (BDI_2249) from Parabact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pw3
TitleCrystal structure of a cysteine protease (BDI_2249) from Parabacteroides distasonis ATCC 8503 at 2.23 A resolution
ComponentsAminopeptidase C
KeywordsHYDROLASE / BLEOMYCIN / CYSTEINE PROTEINASE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


cysteine-type aminopeptidase activity / homocysteine catabolic process / response to toxic substance / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Peptidase C1B, bleomycin hydrolase / Peptidase C1-like family / 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
ACETATE ION / : / Aminopeptidase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.23 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a cysteine protease (BDI_2249) from Parabacteroides distasonis ATCC 8503 at 2.23 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_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_asym_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_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: Aminopeptidase C
B: Aminopeptidase C
C: Aminopeptidase C
D: Aminopeptidase C
E: Aminopeptidase C
F: Aminopeptidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,72648
Polymers265,6276
Non-polymers2,09842
Water36,0842003
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25970 Å2
ΔGint-430 kcal/mol
Surface area80500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.592, 137.810, 223.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Aminopeptidase C / Cysteine protease


Mass: 44271.238 Da / Num. of mol.: 6 / Fragment: sequence database residues 24-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_2249 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LE66

-
Non-polymers , 6 types, 2045 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2003 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE CONSTRUCT (RESIDUES 24-405) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 24-405) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.37 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20.00% polyethylene glycol 3350, 0.2000M potassium sodium tartrate, No Buffer pH 7.2, Additive: 0.001 M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 24, 2010
Details: flat collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.23→29.966 Å / Num. obs: 154800 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.695 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.23-2.310.5342.611568830326199.6
2.31-2.40.4293.211339929527199.6
2.4-2.510.3354.111778530569199.5
2.51-2.640.2545.311504529818199.5
2.64-2.810.1777.411972731005199.3
2.81-3.020.12110.411234529172198.9
3.02-3.330.07615.711807430717198.7
3.33-3.810.04822.811444029826198.3
3.81-4.780.03529.111275529403197.7
4.78-29.9660.03132.511402829501195.5

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.6.0093refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.23→29.966 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 7.033 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. ZINC, POTASSIUM, CHLORIDE, ACETATE (ACT), AND ETHYLENE GLYCOL(EDO) MODELED ARE PRESENT PROTEIN/CRYSTALLIZATION /CRYO BUFFER. 6. NCS RESTRAINTS WERE APPLIED USING REFMAC IMPLEMENTATION OF LOCAL NCS RESTRAINTS (NCS LOCAL).
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 7771 5 %RANDOM
Rwork0.1592 ---
obs0.1603 154749 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.3 Å2 / Biso mean: 40.4993 Å2 / Biso min: 6.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.23→29.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17102 0 87 2003 19192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02217868
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211866
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.93724244
X-RAY DIFFRACTIONr_angle_other_deg1.109328922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88552216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57324.664849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.189152919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5581555
X-RAY DIFFRACTIONr_chiral_restr0.0780.22537
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220123
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023735
LS refinement shellResolution: 2.23→2.287 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 561 -
Rwork0.221 10341 -
all-10902 -
obs--99.09 %
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)
10.2878-0.1097-0.08790.47870.06820.24370.00210.01510.00520.0505-0.0275-0.03140.03760.01070.02540.06990.0051-0.0020.0344-0.00090.03550.8847113.989931.1864
20.1654-0.0608-0.01310.53170.29040.477-0.014-0.02360.02110.0438-0.06330.03530.0313-0.07080.07730.0553-0.02450.01350.053-0.05260.0584-23.7021154.623559.9546
30.9743-0.28750.20690.56830.02190.7021-0.06-0.2807-0.10940.139-0.00980.16940.2375-0.20560.06980.1856-0.11350.10160.1778-0.03960.0768-41.5869123.104560.8234
40.5279-0.0092-0.05780.45110.00970.85040.00410.08050.2071-0.05-0.11970.1124-0.0436-0.20020.11570.01590.0315-0.03970.1077-0.05550.1893-52.9328152.417315.6761
51.05180.25420.22290.43870.19440.50190.09760.0498-0.05690.0323-0.10050.04860.0901-0.09070.00290.0512-0.0118-0.02580.073-0.05080.0675-45.5587117.21838.5885
60.81430.21270.12440.61490.19260.80740.00280.11430.1513-0.08320.0712-0.0041-0.13560.1975-0.0740.0382-0.03530.02690.07360.01010.06160.4684146.931413.3707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 406
2X-RAY DIFFRACTION2B32 - 406
3X-RAY DIFFRACTION3C33 - 406
4X-RAY DIFFRACTION4D32 - 406
5X-RAY DIFFRACTION5E32 - 406
6X-RAY DIFFRACTION6F32 - 406

+
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