[English] 日本語
Yorodumi
- PDB-3fcn: Crystal structure of an alpha-helical protein of unknown function... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fcn
TitleCrystal structure of an alpha-helical protein of unknown function (rru_a3208) from rhodospirillum rubrum atcc 11170 at 1.45 A resolution
Componentsan alpha-helical protein of unknown function (Pfam01724)
KeywordsUNKNOWN FUNCTION / Duf29 family protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyUncharcterised protein PF01724 / Domain of unknown function DUF29 / Malate Synthase G; Chain: A; Domain 4 / Up-down Bundle / Mainly Alpha / DUF29 domain-containing protein
Function and homology information
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an alpha-helical protein of unknown function (Pfam01724) (YP_428290.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
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
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: an alpha-helical protein of unknown function (Pfam01724)


Theoretical massNumber of molelcules
Total (without water)18,7301
Polymers18,7301
Non-polymers00
Water5,386299
1
A: an alpha-helical protein of unknown function (Pfam01724)

A: an alpha-helical protein of unknown function (Pfam01724)


Theoretical massNumber of molelcules
Total (without water)37,4602
Polymers37,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1920 Å2
ΔGint-10 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.707, 54.561, 57.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein an alpha-helical protein of unknown function (Pfam01724)


Mass: 18730.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Gene: Rru_A3208, YP_428290.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2RPE2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0000M NaCitrate, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97882,0.97828
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 12, 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
20.978821
30.978281
ReflectionResolution: 1.45→26.343 Å / Num. obs: 39973 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.896 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 5.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.493.60.5491.31052828990.549100
1.49-1.533.60.4391.71035028450.439100
1.53-1.573.60.3951.91004527590.395100
1.57-1.623.60.3412.2983327000.341100
1.62-1.673.70.282.6947825940.28100
1.67-1.733.60.2492.9927825480.249100
1.73-1.83.60.2113.5886324290.211100
1.8-1.873.60.1714.2858623530.171100
1.87-1.963.60.145.2824222610.14100
1.96-2.053.60.1056.6783921610.105100
2.05-2.163.60.0897.6751320710.089100
2.16-2.293.60.0847.8711719720.084100
2.29-2.453.60.087.8661018360.08100
2.45-2.653.60.0758.4625117270.075100
2.65-2.93.60.0639.8577415940.063100
2.9-3.243.60.05510.6526614550.055100
3.24-3.743.60.05510.6463612880.055100
3.74-4.593.50.05111.8393711100.05199.9
4.59-6.483.50.05311.430428720.05399.4
6.48-29.673.20.04712.215994990.04797.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→26.343 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.18 / SU B: 2.235 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.058
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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2002 5 %RANDOM
Rwork0.161 ---
obs0.162 39934 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.46 Å2 / Biso mean: 17.817 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2---0.16 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.45→26.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 0 299 1546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221506
X-RAY DIFFRACTIONr_bond_other_d0.0010.021078
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9632087
X-RAY DIFFRACTIONr_angle_other_deg0.89232631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7965215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22622.94185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70815281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6941523
X-RAY DIFFRACTIONr_chiral_restr0.0930.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211771
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02332
X-RAY DIFFRACTIONr_mcbond_it1.633903
X-RAY DIFFRACTIONr_mcbond_other0.4553352
X-RAY DIFFRACTIONr_mcangle_it2.63551488
X-RAY DIFFRACTIONr_scbond_it3.9348603
X-RAY DIFFRACTIONr_scangle_it6.00111568
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 135 -
Rwork0.251 2760 -
all-2895 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 22.0339 Å / Origin y: 2.2383 Å / Origin z: 34.1256 Å
111213212223313233
T0.0062 Å2-0.0022 Å20 Å2-0.0018 Å2-0.0012 Å2--0.0038 Å2
L0.3795 °2-0.0717 °20.2273 °2-0.1958 °2-0.0982 °2--0.6527 °2
S0.0129 Å °-0.0182 Å °0.0107 Å °-0.0121 Å °-0.0001 Å °0.0217 Å °0.0054 Å °-0.0096 Å °-0.0128 Å °

+
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