[English] 日本語
Yorodumi
- PDB-4h6v: Structure of Patellamide maturation protease PatA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h6v
TitleStructure of Patellamide maturation protease PatA
ComponentsSubtilisin-like protein
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / Peptidase S8/S53 domain / : / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site ...Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / Peptidase S8/S53 domain / : / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin-like protein
Similarity search - Component
Biological speciesProchloron didemni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsNair, S.K. / Agarwal, V.
CitationJournal: Chem.Biol. / Year: 2012
Title: Structures of cyanobactin maturation enzymes define a family of transamidating proteases.
Authors: Agarwal, V. / Pierce, E. / McIntosh, J. / Schmidt, E.W. / Nair, S.K.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Subtilisin-like protein


Theoretical massNumber of molelcules
Total (without water)32,0171
Polymers32,0171
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.717, 83.717, 42.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Subtilisin-like protein


Mass: 32017.062 Da / Num. of mol.: 1 / Fragment: unp residues 513-866
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochloron didemni (bacteria) / Gene: patA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q52QI9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.31 Å3/Da / Density % sol: 46.83 % / Mosaicity: 0.472 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 31792 / % possible obs: 97.4 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.083 / Χ2: 1.457 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.50.66124260.772175.6
1.76-1.836.20.51932100.832198.7
1.83-1.919.50.42832490.8781100
1.91-2.02120.34932380.981100
2.02-2.1413.80.2832321.1371100
2.14-2.3114.80.20432341.2721100
2.31-2.5415.10.1432761.2821100
2.54-2.9115.10.10732711.7111100
2.91-3.66150.06632732.0931100
3.66-5014.50.04833832.25199.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.387 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 1606 5.1 %RANDOM
Rwork0.21 ---
obs0.2116 31753 97.71 %-
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: 59.81 Å2 / Biso mean: 28.5278 Å2 / Biso min: 11.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 0 237 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212030
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9682764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2845270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65324.36887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13715308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5921515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211567
X-RAY DIFFRACTIONr_mcbond_it0.6971.51343
X-RAY DIFFRACTIONr_mcangle_it1.30122140
X-RAY DIFFRACTIONr_scbond_it1.7473687
X-RAY DIFFRACTIONr_scangle_it2.9174.5624
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 93 -
Rwork0.332 1658 -
all-1751 -
obs--73.63 %

+
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