[English] 日本語
Yorodumi
- PDB-1yem: Conserved hypothetical protein Pfu-838710-001 from Pyrococcus furiosus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yem
TitleConserved hypothetical protein Pfu-838710-001 from Pyrococcus furiosus
ComponentsConserved hypothetical protein Pfu-838710-001
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Southeast Collaboratory for Structural Genomics / SECSG / Protein Structure Initiative / PSI / conserved hypothetical protein / Pyrococcus furiosus / hyperthermophile
Function / homology
Function and homology information


Adenylyl cyclase CyaB / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 2.3 Å
AuthorsYang, H. / Chang, J. / Shah, A. / Ng, J.D. / Liu, Z.-J. / Chen, L. / Lee, D. / Tempel, W. / Praissman, J.L. / Lin, D. ...Yang, H. / Chang, J. / Shah, A. / Ng, J.D. / Liu, Z.-J. / Chen, L. / Lee, D. / Tempel, W. / Praissman, J.L. / Lin, D. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Jenney Jr., F.E. / Adams, M.W.W. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Conserved hypothetical protein Pfu-838710-001 from Pyrococcus furiosus
Authors: Yang, H. / Chang, J. / Shah, A. / Ng, J.D. / Liu, Z.-J. / Chen, L. / Lee, D. / Tempel, W. / Praissman, J.L. / Lin, D. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Jenney Jr., ...Authors: Yang, H. / Chang, J. / Shah, A. / Ng, J.D. / Liu, Z.-J. / Chen, L. / Lee, D. / Tempel, W. / Praissman, J.L. / Lin, D. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Jenney Jr., F.E. / Adams, M.W.W. / Rose, J.P. / Wang, B.-C.
History
DepositionDec 28, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionJan 11, 2005ID: 1XKC
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.4Oct 11, 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
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conserved hypothetical protein Pfu-838710-001
B: Conserved hypothetical protein Pfu-838710-001
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,03410
Polymers42,8392
Non-polymers1958
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-37 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.016, 97.016, 127.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsnot known

-
Components

#1: Protein Conserved hypothetical protein Pfu-838710-001


Mass: 21419.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0863 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U2H2
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.05 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 313 K / Method: modified microbatch / pH: 7.9
Details: 1.2M sodium dihydrogen phosphate, 1.2M potassium dihydrogen sulfate, 0.1M TRIS, pH 7.9, modified microbatch, temperature 313K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.06 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 28161 / % possible obs: 89.2 % / Rmerge(I) obs: 0.065 / Χ2: 1.338
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
2.3-2.380.1612870.78741.5
2.38-2.480.17120060.71464.4
2.48-2.590.15926970.886.3
2.59-2.730.15630600.79598.5
2.73-2.90.12231280.87100
2.9-3.120.08931340.993100
3.12-3.440.06731381.295100
3.44-3.930.06231701.497100
3.93-4.950.06132042.063100
4.95-400.05733371.99499.8

-
Phasing

PhasingMethod: sad
Phasing MADD res high: 3.7 Å / D res low: 20 Å / FOM : 0.43 / Reflection: 7306
Phasing MAD shell
Resolution (Å)FOM Reflection
11.62-200.42349
7.92-11.620.47665
6.37-7.920.48812
5.47-6.370.45909
4.86-5.470.451019
4.43-4.860.431123
4.09-4.430.41185
3.82-4.090.41244
Phasing dmFOM : 0.58 / FOM acentric: 0.61 / FOM centric: 0.37 / Reflection: 8579 / Reflection acentric: 7504 / Reflection centric: 1075
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10-13.9540.840.840.5126618878
6.3-100.750.810.491237994243
5-6.30.690.740.3714911290201
4.4-50.690.720.414651297168
3.8-4.40.580.610.3125682313255
3.5-3.80.210.210.1515521422130

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
RefinementMethod to determine structure: SAS / Resolution: 2.3→37.932 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.228 / SU B: 6.057 / SU ML: 0.145 / SU R Cruickshank DPI: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.2 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 1450 5.16 %Thin shells
Rwork0.2228 ---
all0.225 ---
obs0.22461 28102 89.468 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 44.002 Å2
Baniso -1Baniso -2Baniso -3
1-1.283 Å20.642 Å20 Å2
2--1.283 Å20 Å2
3----1.925 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 8 17 2721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222754
X-RAY DIFFRACTIONr_bond_other_d0.0020.022525
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.9643726
X-RAY DIFFRACTIONr_angle_other_deg0.68335835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7555327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18324.825143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64515488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0531514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
X-RAY DIFFRACTIONr_nbd_refined0.2010.2413
X-RAY DIFFRACTIONr_nbd_other0.1690.22322
X-RAY DIFFRACTIONr_nbtor_refined0.180.21310
X-RAY DIFFRACTIONr_nbtor_other0.0790.21712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0530.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.24
X-RAY DIFFRACTIONr_mcbond_it2.21621693
X-RAY DIFFRACTIONr_mcbond_other0.4222666
X-RAY DIFFRACTIONr_mcangle_it3.41732657
X-RAY DIFFRACTIONr_mcangle_other1.91232230
X-RAY DIFFRACTIONr_scbond_it1.91421218
X-RAY DIFFRACTIONr_scbond_other0.55922318
X-RAY DIFFRACTIONr_scangle_it3.14131069
X-RAY DIFFRACTIONr_scangle_other1.4433605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.360.415580.294848228739.615
2.36-2.4240.291580.2951185223455.64
2.424-2.4940.339870.3011467214872.346
2.494-2.570.337870.2891751211187.068
2.57-2.6540.307870.2851888203297.195
2.654-2.7470.3631160.2831843196999.492
2.747-2.850.263870.27918531940100
2.85-2.9660.3291160.27317331849100
2.966-3.0970.329870.2616681755100
3.097-3.2470.296870.23816181705100
3.247-3.4210.26870.21215311618100
3.421-3.6270.261580.22414731531100
3.627-3.8750.253870.20113681455100
3.875-4.1810.22580.18112801338100
4.181-4.5750.189870.16111731260100
4.575-5.1060.189580.1610911149100
5.106-5.8780.256290.2149791008100
5.878-7.1560.258580.234821879100
7.156-9.9450.252290.209674703100
9.945-37.9320.205290.28340843999.544

+
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