[English] 日本語
Yorodumi
- PDB-8u5a: Improving protein expression, stability, and function with ProteinMPNN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u5a
TitleImproving protein expression, stability, and function with ProteinMPNN
ComponentsDesigned myoglobin
KeywordsDE NOVO PROTEIN / protein expression / stability / function / ProteinMPNN / De novo design
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKalvet, I. / Bera, A.K. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Improving Protein Expression, Stability, and Function with ProteinMPNN.
Authors: Sumida, K.H. / Nunez-Franco, R. / Kalvet, I. / Pellock, S.J. / Wicky, B.I.M. / Milles, L.F. / Dauparas, J. / Wang, J. / Kipnis, Y. / Jameson, N. / Kang, A. / De La Cruz, J. / Sankaran, B. / ...Authors: Sumida, K.H. / Nunez-Franco, R. / Kalvet, I. / Pellock, S.J. / Wicky, B.I.M. / Milles, L.F. / Dauparas, J. / Wang, J. / Kipnis, Y. / Jameson, N. / Kang, A. / De La Cruz, J. / Sankaran, B. / Bera, A.K. / Jimenez-Oses, G. / Baker, D.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Designed myoglobin
B: Designed myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2114
Polymers38,9782
Non-polymers1,2332
Water1,53185
1
A: Designed myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1052
Polymers19,4891
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Designed myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1052
Polymers19,4891
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.589, 41.669, 128.439
Angle α, β, γ (deg.)90.000, 95.130, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Designed myoglobin


Mass: 19489.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH 6.5, 28% w/v Polyethylene glycol monomethyl ether 2,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→42.64 Å / Num. obs: 22200 / % possible obs: 97.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 36.01 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0753 / Rpim(I) all: 0.0404 / Net I/σ(I): 10.95
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 1513 / CC1/2: 0.773 / Rpim(I) all: 0.551 / % possible all: 95.52

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.64 Å / SU ML: 0.297 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2614 1984 8.94 %
Rwork0.2276 20216 -
obs0.2307 22200 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.71 Å2
Refinement stepCycle: LAST / Resolution: 2→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 86 85 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232588
X-RAY DIFFRACTIONf_angle_d0.52213512
X-RAY DIFFRACTIONf_chiral_restr0.0323366
X-RAY DIFFRACTIONf_plane_restr0.0037446
X-RAY DIFFRACTIONf_dihedral_angle_d16.569976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.40061410.34531372X-RAY DIFFRACTION95.58
2.05-2.110.3561410.32961429X-RAY DIFFRACTION94.69
2.11-2.170.2821370.27051412X-RAY DIFFRACTION97.54
2.17-2.240.33261350.26861423X-RAY DIFFRACTION97.25
2.24-2.320.37941390.31031365X-RAY DIFFRACTION93.65
2.32-2.410.2721380.2381459X-RAY DIFFRACTION98.04
2.41-2.520.28751470.22881447X-RAY DIFFRACTION98.03
2.52-2.650.29721430.24631452X-RAY DIFFRACTION98.09
2.65-2.820.29311440.2341446X-RAY DIFFRACTION97.79
2.82-3.040.27941370.23911443X-RAY DIFFRACTION97.71
3.04-3.340.25231460.23981459X-RAY DIFFRACTION98.77
3.34-3.820.23981460.19791472X-RAY DIFFRACTION97.82
3.83-4.820.20931480.18561483X-RAY DIFFRACTION98.37
4.82-42.640.24481420.22191554X-RAY DIFFRACTION99.01

+
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