[English] 日本語
Yorodumi
- PDB-3qfw: Crystal structure of Rubisco-like protein from Rhodopseudomonas p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qfw
TitleCrystal structure of Rubisco-like protein from Rhodopseudomonas palustris
ComponentsRibulose-1,5-bisphosphate carboxylase/oxygenase large subunit
KeywordsLYASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / RLP fold
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel ...Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.789 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Gerlt, J.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Rubisco-like protein from Rhodopseudomonas palustris
Authors: Fedorov, A.A. / Fedorov, E.V. / Gerlt, J.A. / Burley, S.K. / Almo, S.C.
History
DepositionJan 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
B: Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9098
Polymers79,3332
Non-polymers5766
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-95 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.440, 119.217, 66.856
Angle α, β, γ (deg.)90.00, 115.46, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit / RUBISCO-LIKE PROTEIN


Mass: 39666.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: BisB18 / Gene: RPC_2184 / Production host: Escherichia coli (E. coli)
References: UniProt: Q216E8, ribulose-bisphosphate carboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0,1M Bis-Tris, 0.2M Lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.789→27.921 Å / Num. all: 71923 / Num. obs: 71923 / % possible obs: 94.08 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.12 Å2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.789→27.921 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 32.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3639 5.06 %RANDOM
Rwork0.2436 ---
all0.2457 71923 --
obs0.2457 71923 94.08 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.931 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.7748 Å2-0 Å2-1.5699 Å2
2--2.5732 Å2-0 Å2
3----17.3481 Å2
Refinement stepCycle: LAST / Resolution: 1.789→27.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5165 0 30 212 5407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075293
X-RAY DIFFRACTIONf_angle_d1.0427188
X-RAY DIFFRACTIONf_dihedral_angle_d13.6621920
X-RAY DIFFRACTIONf_chiral_restr0.067835
X-RAY DIFFRACTIONf_plane_restr0.005948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7891-1.81270.3104710.31671580X-RAY DIFFRACTION56
1.8127-1.83750.3405920.29792027X-RAY DIFFRACTION73
1.8375-1.86370.32371180.29342291X-RAY DIFFRACTION81
1.8637-1.89150.3351600.29482619X-RAY DIFFRACTION95
1.8915-1.92110.33881490.27662725X-RAY DIFFRACTION97
1.9211-1.95260.31011510.26542683X-RAY DIFFRACTION97
1.9526-1.98620.27041420.24852719X-RAY DIFFRACTION97
1.9862-2.02230.33491290.24692727X-RAY DIFFRACTION97
2.0223-2.06120.30541460.25082724X-RAY DIFFRACTION98
2.0612-2.10330.30041420.2542711X-RAY DIFFRACTION98
2.1033-2.1490.31531630.2382701X-RAY DIFFRACTION98
2.149-2.1990.27841670.24062707X-RAY DIFFRACTION98
2.199-2.25390.3291570.24682696X-RAY DIFFRACTION98
2.2539-2.31490.28141460.23032754X-RAY DIFFRACTION98
2.3149-2.38290.26791610.22662736X-RAY DIFFRACTION98
2.3829-2.45980.27941370.22612716X-RAY DIFFRACTION99
2.4598-2.54770.27581300.23442757X-RAY DIFFRACTION98
2.5477-2.64960.28321200.25522787X-RAY DIFFRACTION99
2.6496-2.77010.28151630.24932746X-RAY DIFFRACTION99
2.7701-2.9160.24751330.24342792X-RAY DIFFRACTION99
2.916-3.09850.29451430.25122753X-RAY DIFFRACTION99
3.0985-3.33730.28481620.26012749X-RAY DIFFRACTION99
3.3373-3.67250.29441380.2432725X-RAY DIFFRACTION98
3.6725-4.20240.28541620.22622617X-RAY DIFFRACTION94
4.2024-5.28870.23341200.21672608X-RAY DIFFRACTION92
5.2887-27.92460.29321370.262634X-RAY DIFFRACTION93

+
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