[English] 日本語
Yorodumi
- PDB-3pro: ALPHA-LYTIC PROTEASE COMPLEXED WITH C-TERMINAL TRUNCATED PRO REGION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pro
TitleALPHA-LYTIC PROTEASE COMPLEXED WITH C-TERMINAL TRUNCATED PRO REGION
Components(ALPHA-LYTIC PROTEASE) x 2
Keywordshydrolase/hydrolase inhibitor / PRO REGION / FOLDASE / PROTEIN FOLDING / SERINE PROTEASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #50 / Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / GMP Synthetase; Chain A, domain 3 / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain ...GMP Synthetase; Chain A, domain 3 - #50 / Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / GMP Synthetase; Chain A, domain 3 / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSauter, N.K. / Mau, T. / Rader, S.D. / Agard, D.A.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structure of alpha-lytic protease complexed with its pro region.
Authors: Sauter, N.K. / Mau, T. / Rader, S.D. / Agard, D.A.
History
DepositionAug 26, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2012Group: Non-polymer description
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: ALPHA-LYTIC PROTEASE
C: ALPHA-LYTIC PROTEASE
B: ALPHA-LYTIC PROTEASE
D: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7086
Polymers75,3024
Non-polymers4062
Water5,783321
1
A: ALPHA-LYTIC PROTEASE
C: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8543
Polymers37,6512
Non-polymers2031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-10 kcal/mol
Surface area13900 Å2
MethodPISA
2
B: ALPHA-LYTIC PROTEASE
D: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8543
Polymers37,6512
Non-polymers2031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-8 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 101.000, 72.140
Angle α, β, γ (deg.)90.00, 109.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9972, -0.069044, -0.028735), (0.068494, 0.997457, -0.01972), (0.030023, 0.017697, 0.999392)
Vector: 15.57713, 50.66458, 12.83321)

-
Components

#1: Protein ALPHA-LYTIC PROTEASE


Mass: 19815.014 Da / Num. of mol.: 2 / Fragment: MATURE PROTEASE / Mutation: M158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Cell line: B834 / Plasmid: PT7PRO-3 / Cellular location (production host): CULTURE FILTRATE / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P00778
#2: Protein ALPHA-LYTIC PROTEASE


Mass: 17835.881 Da / Num. of mol.: 2 / Fragment: PRO REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Description: T7 EXPRESSION SYSTEM / Cell line: B834 / Plasmid: PT7PRO-3 / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P00778
#3: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.79 Å3/Da / Density % sol: 56 %
Description: STATISTICS INCLUDE 78512 MEASUREMENTS MADE ON ROTATING ANODE SOURCE
Crystal growpH: 6.25 / Details: pH 6.25
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 7 ℃ / pH: 8 / Method: vapor diffusion / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
20.34 Mlithium sulfate1drop
32.3 %glycerol1drop
42 mMdithiothreitol1drop
52.7 mMMES1drop
615 mMcitric acid1reservoirbufferA
730 mMphosphoric acid1reservoirbufferA
826 mMorthoboric acid1reservoirbufferA
90.155 Msodium hydroxide1reservoirbufferA
100.8 Mlithium sulfate1reservoirbufferA
115 %glycerol1reservoirbufferA
12bufferA1drop0.45 times

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 5, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→67.4 Å / Num. obs: 255283 / % possible obs: 96.5 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.6 / % possible all: 95.5
Reflection
*PLUS
Num. obs: 73741 / Num. measured all: 176771
Reflection shell
*PLUS
% possible obs: 95.5 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.854refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TAL

1tal


Resolution: 1.8→67.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 -10 %RANDOM
Rwork0.207 ---
obs0.207 73722 96.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→67.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5018 0 24 321 5363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.81 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.25 / Total num. of bins used: 50
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.854 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rwork: 0.25

+
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