[English] 日本語
Yorodumi
- PDB-3fez: Crystal structure of uncharacterized ferredoxin fold protein rela... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fez
TitleCrystal structure of uncharacterized ferredoxin fold protein related to antibiotic biosynthesis monooxygenases (YP_014836.1) from LISTERIA MONOCYTOGENES 4b F2365 at 2.10 A resolution
Componentsuncharacterized ferredoxin fold protein related to antibiotic biosynthesis monooxygenases
Keywordsstructural genomics / unknown function / YP_014836.1 / uncharacterized ferredoxin fold protein related to antibiotic biosynthesis monooxygenases / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyAlpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesListeria monocytogenes str. 4b F2365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized ferredoxin fold protein related to antibiotic biosynthesis monooxygenases (YP_014836.1) from LISTERIA MONOCYTOGENES 4b F2365 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.5Oct 30, 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: uncharacterized ferredoxin fold protein related to antibiotic biosynthesis monooxygenases


Theoretical massNumber of molelcules
Total (without water)22,1181
Polymers22,1181
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.220, 73.220, 214.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein uncharacterized ferredoxin fold protein related to antibiotic biosynthesis monooxygenases


Mass: 22117.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes str. 4b F2365 (bacteria)
Gene: LMOf2365_2246, YP_014836.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q71XF2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2000M NH4H2PO3, 20.0000% PEG-3350, No Buffer pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97966
DetectorType: MAR MAR300 / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979661
ReflectionResolution: 2.1→28.976 Å / Num. obs: 20290 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.004 Å2 / Rmerge(I) obs: 0.155
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.171.621608320591.5
2.17-2.262.329528384598.2
2.26-2.363.428541363698.4
2.36-2.494.330273385998.6
2.49-2.645.728015356898.6
2.64-2.857.833518383398.7
2.85-3.1311.239385363798.9
3.13-3.5916.849991380199
3.59-4.5122.349700370399.1
4.5124.749994376197.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→28.976 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 7.22 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.138
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE 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 THE 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1039 5.1 %RANDOM
Rwork0.203 ---
obs0.204 20282 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 87.59 Å2 / Biso mean: 53.552 Å2 / Biso min: 39.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 0 84 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221475
X-RAY DIFFRACTIONr_bond_other_d0.0010.02987
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9311999
X-RAY DIFFRACTIONr_angle_other_deg0.77132407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3335184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.36924.44472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26215256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.94155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02324
X-RAY DIFFRACTIONr_nbd_refined0.2350.3289
X-RAY DIFFRACTIONr_nbd_other0.1840.3950
X-RAY DIFFRACTIONr_nbtor_refined0.1920.5720
X-RAY DIFFRACTIONr_nbtor_other0.0890.5739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.5124
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0350.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.514
X-RAY DIFFRACTIONr_mcbond_it0.8431.5956
X-RAY DIFFRACTIONr_mcbond_other0.1441.5363
X-RAY DIFFRACTIONr_mcangle_it1.24221435
X-RAY DIFFRACTIONr_scbond_it1.723655
X-RAY DIFFRACTIONr_scangle_it2.3434.5564
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 73 -
Rwork0.241 1287 -
all-1360 -
obs--91.28 %
Refinement TLS params.Method: refined / Origin x: 61.94 Å / Origin y: 14.3165 Å / Origin z: 17.2999 Å
111213212223313233
T-0.0582 Å20.1047 Å2-0.0192 Å2--0.1401 Å20.0069 Å2---0.1133 Å2
L1.5646 °2-1.1572 °2-0.6955 °2-4.0281 °2-0.0715 °2--3.4719 °2
S0.0207 Å °-0.0377 Å °0.0207 Å °-0.2048 Å °0.0712 Å °0.0658 Å °-0.3457 Å °-0.1386 Å °-0.0919 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