[English] 日本語
Yorodumi
- PDB-2pv4: CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM DUF3069 FAMI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pv4
TitleCRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM DUF3069 FAMILY (SAMA_2622) FROM SHEWANELLA AMAZONENSIS SB2B AT 1.95 A RESOLUTION
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologySama2622-like fold / Sama2622-like / Protein of unknown function DUF3069 / Sama2622-like superfamily / Protein of unknown function (DUF3069) / Orthogonal Bundle / Mainly Alpha / DUF3069 domain-containing protein
Function and homology information
Biological speciesShewanella amazonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (YP_928494.1) from Shewanella amazonensis SB2B at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7613
Polymers16,5771
Non-polymers1842
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.957, 47.283, 98.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Uncharacterized protein


Mass: 16577.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: SB2B / Gene: YP_928494.1, Sama_2622 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S8W8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 2.4M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97936, 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979361
30.979221
ReflectionResolution: 1.95→29.062 Å / Num. obs: 12889 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 35.56 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-240.6041.337699420.604100
2-2.0640.4881.636549110.488100
2.06-2.1240.3831.935248840.383100
2.12-2.1840.2972.534178500.297100
2.18-2.2540.2582.733518470.258100
2.25-2.3340.2253.231567880.225100
2.33-2.4240.1524.831347860.152100
2.42-2.5240.1345.330247560.134100
2.52-2.6340.1156.128917280.115100
2.63-2.763.90.0986.927707020.098100
2.76-2.9140.0917.126016540.091100
2.91-3.083.90.0837.724766320.083100
3.08-3.33.90.078.823876110.07100
3.3-3.563.90.0599.921395460.059100
3.56-3.93.90.0511220125180.051100
3.9-4.363.80.04713.218254760.047100
4.36-5.033.80.05211.516084250.052100
5.03-6.173.60.05510.413353680.055100
6.17-8.723.50.04214.110302920.04299.9
8.72-29.0630.03518.45251730.03595.2

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.062 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.71 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.158
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 5. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE 62 WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 627 4.9 %RANDOM
Rwork0.205 ---
all0.208 ---
obs0.208 12845 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2---0.18 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 12 71 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221196
X-RAY DIFFRACTIONr_bond_other_d0.0010.02811
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9681622
X-RAY DIFFRACTIONr_angle_other_deg1.00731969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9345156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72723.77453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17815206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2331511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021370
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02250
X-RAY DIFFRACTIONr_nbd_refined0.220.2305
X-RAY DIFFRACTIONr_nbd_other0.1820.2830
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2615
X-RAY DIFFRACTIONr_nbtor_other0.090.2607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.29
X-RAY DIFFRACTIONr_mcbond_it2.213789
X-RAY DIFFRACTIONr_mcbond_other0.5473305
X-RAY DIFFRACTIONr_mcangle_it3.47551212
X-RAY DIFFRACTIONr_scbond_it5.5728476
X-RAY DIFFRACTIONr_scangle_it7.65411410
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 46 -
Rwork0.281 897 -
obs-943 100 %
Refinement TLS params.Method: refined / Origin x: 35.6117 Å / Origin y: 42.798 Å / Origin z: 9.4737 Å
111213212223313233
T-0.0728 Å20.0079 Å2-0.0091 Å2--0.0644 Å2-0.0534 Å2---0.0283 Å2
L0.6516 °20.4619 °20.116 °2-2.1066 °21.0406 °2--2.2875 °2
S0.0088 Å °0.032 Å °-0.1561 Å °-0.1444 Å °-0.0984 Å °0.3315 Å °-0.2922 Å °-0.0537 Å °0.0896 Å °
Refinement TLS groupSelection: ALL

+
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