[English] 日本語
Yorodumi
- PDB-3eo6: Crystal structure of protein of unknown function (DUF1255) (AFE_2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eo6
TitleCrystal structure of protein of unknown function (DUF1255) (AFE_2634) from ACIDITHIOBACILLUS FERROOXIDANS NCIB8455 at 0.97 A resolution
Componentsprotein of unknown function (DUF1255)
Keywordsstructural genomics / unknown function / AFE_2634 / protein of unknown function (DUF1255) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyJelly Rolls / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesAcidithiobacillus ferrooxidans ATCC 23270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.97 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function (DUF1255) (AFE_2634) from ACIDITHIOBACILLUS FERROOXIDANS NCIB8455 at 0.97 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: protein of unknown function (DUF1255)
B: protein of unknown function (DUF1255)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5255
Polymers23,3552
Non-polymers1713
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-25 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.785, 82.028, 40.847
Angle α, β, γ (deg.)90.000, 109.950, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 6 / Auth seq-ID: 0 - 105 / Label seq-ID: 1 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein protein of unknown function (DUF1255)


Mass: 11677.310 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans ATCC 23270 (bacteria)
Gene: AFE_2634 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details(1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...(1) 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. (2) THE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT-KB DATABASE AT THE TIME OF DEPOSITION. IT IS AVAILABLE AS LOCUS ID AFE_2634 FROM THE COMPREHENSIVE MICROBIAL RESOURCE AT THE J. CRAIG VENTER INSTITUTE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M MgCl2, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 1, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978371
ReflectionResolution: 0.97→28.194 Å / Num. obs: 111566 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 7.317 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 5.911
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
0.97-13.50.7031.12885381650.70398
1-1.023.60.5161.52820979430.51698.3
1.02-1.053.60.3822751077360.3898.5
1.05-1.083.60.2892.62670474680.28998.9
1.08-1.123.60.2093.62635073430.20999.1
1.12-1.163.60.1614.62574171330.16199.3
1.16-1.23.60.1425.12491368850.14299.6
1.2-1.253.60.1335.32399766000.13399.7
1.25-1.313.70.1225.72331563850.12299.9
1.31-1.373.70.1086.42237360960.108100
1.37-1.453.70.0937.32141858030.093100
1.45-1.533.70.0798.52039355040.079100
1.53-1.643.70.0719.11924951450.071100
1.64-1.774.20.079.11992347870.07100
1.77-1.944.90.0738.42176144570.073100
1.94-2.176.30.0629.92519139940.062100
2.17-2.57.40.06210.62634435410.062100
2.5-3.077.50.05411.52240530010.054100
3.07-4.346.80.04812.91584423210.04899.9
4.34-28.946.20.0512.7774912590.0597.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHARPphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 0.97→28.194 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / Occupancy max: 1 / Occupancy min: 0.11 / SU B: 0.613 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 ~0.8 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. U VALUES WERE REFINED INDIVIDUALLY 4. TRIS (TRS) AND MG MODELED WERE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. THE DENSITY FOR N-TERMINUS AND C-TERMINUS ARE POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.143 5605 5 %RANDOM
Rwork0.123 ---
obs0.124 111533 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.85 Å2 / Biso mean: 11.791 Å2 / Biso min: 3.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.2 Å2
2---0.26 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 0.97→28.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 10 454 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212313
X-RAY DIFFRACTIONr_bond_other_d0.0010.021512
X-RAY DIFFRACTIONr_angle_refined_deg1.921.9833210
X-RAY DIFFRACTIONr_angle_other_deg0.97333740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3255336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19424.059101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22615405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6821519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212872
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02463
X-RAY DIFFRACTIONr_mcbond_it2.25531499
X-RAY DIFFRACTIONr_mcbond_other1.4673583
X-RAY DIFFRACTIONr_mcangle_it3.18252480
X-RAY DIFFRACTIONr_scbond_it4.3278814
X-RAY DIFFRACTIONr_scangle_it5.46411730
X-RAY DIFFRACTIONr_rigid_bond_restr1.90233825
X-RAY DIFFRACTIONr_sphericity_free10.2763456
X-RAY DIFFRACTIONr_sphericity_bonded4.00133747
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1074 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.75
LOOSE THERMAL2.0610
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 425 -
Rwork0.331 7737 -
all-8162 -
obs--98.03 %

+
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