[English] 日本語
Yorodumi
- PDB-7qp3: Pseudogymnoascus pannorum M36 protease without the propeptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qp3
TitlePseudogymnoascus pannorum M36 protease without the propeptide
ComponentsExtracellular metalloproteinase
KeywordsRECOMBINATION / Keratinase / Protease / Metalloprotein
Function / homology2-acetamido-2-deoxy-alpha-D-galactopyranose
Function and homology information
Biological speciesPseudogymnoascus pannorum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWilkens, C. / Qiu, J. / Meyer, A.S. / Morth, J.P.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Chinese Scholarship Council201806910049
Other government Denmark
CitationJournal: To Be Published
Title: Phaeosphaeria nodorum M36 protease without the propeptide
Authors: Wilkens, C. / Qiu, J. / Meyer, A.S. / Morth, J.P.
History
DepositionDec 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Extracellular metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9439
Polymers42,2171
Non-polymers7258
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-67 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.080, 67.490, 130.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Extracellular metalloproteinase


Mass: 42217.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudogymnoascus pannorum (fungus) / Production host: Komagataella pastoris (fungus)
References: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#3: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 433 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M potassium thiocyanate, 30% polyethylene glycol monomethyl ether 2,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.84→46.93 Å / Num. obs: 30553 / % possible obs: 99.7 % / Redundancy: 12.57 % / Biso Wilson estimate: 22.38 Å2 / CC1/2: 1 / Net I/σ(I): 8.93
Reflection shellResolution: 1.84→1.96 Å / Num. unique obs: 4782 / CC1/2: 0.37

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBE3data collection
Cootmodel building
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k90

4k90


Resolution: 1.85→46.93 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1998 1525 5 %
Rwork0.1489 28971 -
obs0.1514 30496 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.37 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 35 426 3428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013096
X-RAY DIFFRACTIONf_angle_d1.01584215
X-RAY DIFFRACTIONf_chiral_restr0.0558444
X-RAY DIFFRACTIONf_plane_restr0.0076557
X-RAY DIFFRACTIONf_dihedral_angle_d13.77541097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.35481350.30822568X-RAY DIFFRACTION99.7
1.91-1.970.32411370.24112598X-RAY DIFFRACTION100
1.97-2.050.26581370.1972610X-RAY DIFFRACTION100
2.05-2.150.23141350.18182575X-RAY DIFFRACTION99.96
2.15-2.260.20891380.15492603X-RAY DIFFRACTION100
2.26-2.40.21881360.13532603X-RAY DIFFRACTION100
2.4-2.590.17311390.1312634X-RAY DIFFRACTION100
2.59-2.850.20071380.13462613X-RAY DIFFRACTION100
2.85-3.260.20131410.13352682X-RAY DIFFRACTION100
3.26-4.110.17271400.12282662X-RAY DIFFRACTION99.93
4.11-46.930.15611490.13682823X-RAY DIFFRACTION99.93
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)
12.944588655950.510674236591-0.7012392516341.026457096850.01490839610451.34443333631-0.0146131878718-0.03809123621140.008535594275250.0310152353927-0.0137467027412-0.0375240018858-0.0486656806650.006067570743660.01916868078290.1895194833770.0115674586068-0.02331003347080.1471130384290.009984636456340.1444688492759.7527809045519.335804498853.5808997842
23.679445541070.809628796146-1.06350428861.38942225674-0.7244431673341.89847708147-0.06205920453310.0909403807858-0.127798152186-0.0500759241565-0.0186541730101-0.03489268418940.10457126369-0.006840588428280.08232303572970.2034431105090.00491336246423-0.005043465300460.140149970998-0.02506629300540.1506397509536.3781204994911.963155635444.0340984365
30.582295836440.1218530295020.02493399340740.7686955806880.2185792955151.36900061681-0.01186542627210.002746879138050.0852238034939-0.00261362151301-0.02074220751320.0464814419682-0.0717789921610.009960632081280.02811144678030.204884175666-0.00658008918952-0.015979218720.1628382161170.01144630050050.1985524149316.2277323554344.64557924247.5117489149
45.469306743072.746106206484.750149850114.174854272814.327605041385.53574443310.0908272188654-0.2772543388860.146698532950.18244231696-0.0923297546375-0.02457640510840.171605913566-0.355109865079-0.008270393032050.159095575536-0.003934570563650.02199352883910.13717980978-0.008362107455070.197095742871.2156879354140.442631026661.7555437624
51.51407146573-0.03837066813931.051418123531.25576439028-0.0176293151971.75223950324-0.0153155434610.02475633441370.0291686177216-0.0059269147393-0.03149120154750.0084966304908-0.001313034867350.08725327443020.05044501530980.20106496872-0.01243414289490.0136636201550.1701587751590.001126349253910.1597142239994.7719140234326.920700423351.1446926549
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 245 through 313 )245 - 313245 - 313
22chain 'A' and (resid 314 through 391 )314 - 391314 - 391
33chain 'A' and (resid 1 through 159 )1 - 1591 - 159
44chain 'A' and (resid 160 through 178 )160 - 178160 - 178
55chain 'A' and (resid 179 through 244 )179 - 244179 - 244

+
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