[English] 日本語
Yorodumi
- PDB-3lyu: Crystal Structure of the C-terminal domain (residues 83-215) of P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lyu
TitleCrystal Structure of the C-terminal domain (residues 83-215) of PF1911 hydrogenase from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR246A
ComponentsPutative hydrogenase
KeywordsOXIDOREDUCTASE / The C-terminal has an alpha-beta fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


pyrimidine nucleotide biosynthetic process / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target PfR246A
Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative hydrogenase
B: Putative hydrogenase
C: Putative hydrogenase
D: Putative hydrogenase
E: Putative hydrogenase
F: Putative hydrogenase


Theoretical massNumber of molelcules
Total (without water)98,4786
Polymers98,4786
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-103 kcal/mol
Surface area30650 Å2
MethodPISA
2
A: Putative hydrogenase
B: Putative hydrogenase


Theoretical massNumber of molelcules
Total (without water)32,8262
Polymers32,8262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-25 kcal/mol
Surface area11800 Å2
MethodPISA
3
C: Putative hydrogenase
D: Putative hydrogenase


Theoretical massNumber of molelcules
Total (without water)32,8262
Polymers32,8262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-25 kcal/mol
Surface area11690 Å2
MethodPISA
4
E: Putative hydrogenase
F: Putative hydrogenase


Theoretical massNumber of molelcules
Total (without water)32,8262
Polymers32,8262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-24 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.654, 77.654, 117.513
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
DetailsAccording to the static light scattering data, the C-terminal hydrogenase is dimer in solution, whereas in the crystal forms a hexameric ring.

-
Components

#1: Protein
Putative hydrogenase /


Mass: 16413.072 Da / Num. of mol.: 6 / Fragment: sequence database residues 83-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1911 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8TZS3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M MES (pH 6.5), 18% PEG3350, and 0.2M calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97885 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 8, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.497
11K, H, -L20.503
ReflectionResolution: 2.3→30 Å / Num. all: 70503 / Num. obs: 70362 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.088 / Net I/σ(I): 20.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6941 / Rsym value: 0.368 / % possible all: 99.7

-
Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBfollowed by SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 396034.719 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: TWIN DETAILS NUMBER OF TWIN DOMAINS : 2 TWIN DOMAIN : 1 TWIN OPERATOR : H, K, L TWIN FRACTION : 0.497 TWIN DOMAIN : 2 TWIN OPERATOR : K, H, -L TWIN FRACTION : 0.503
RfactorNum. reflection% reflectionSelection details
Rfree0.237 6048 8.6 %RANDOM
Rwork0.21 ---
all0.219 70373 --
obs0.215 65588 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.276 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.91 Å20 Å20 Å2
2---7.91 Å20 Å2
3---15.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6211 0 0 69 6280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.283 490 9.3 %
Rwork0.267 4782 -
obs-5272 75.2 %

+
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