[English] 日本語
Yorodumi
- PDB-3eof: Crystal structure of putative oxidoreductase (YP_213212.1) from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eof
TitleCrystal structure of putative oxidoreductase (YP_213212.1) from Bacteroides fragilis NCTC 9343 at 1.99 A resolution
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / YP_213212.1 / putative oxidoreductase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Flavin oxidoreductase Frp family / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Oxidase
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative oxidoreductase (YP_213212.1) from Bacteroides fragilis NCTC 9343 at 1.99 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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 / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8144
Polymers57,9012
Non-polymers9132
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-86 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.370, 80.820, 101.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 6 / Auth seq-ID: 2 - 247 / Label seq-ID: 3 - 248

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THAT THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS.

-
Components

#1: Protein Putative oxidoreductase


Mass: 28950.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: YP_213212.1, BF3618 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5L9C9
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.0000% iso-Propanol, 20.0000% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97845
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 7, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 1.99→28.76 Å / Num. obs: 39369 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.84 % / Biso Wilson estimate: 23.863 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.01-2.080.6571.6154336247184.7
2.08-2.170.4912.2207108025198
2.17-2.260.4032.8176536838197.8
2.26-2.380.3213.3194057481198.2
2.38-2.530.2524.1196187558198.4
2.53-2.730.1885.3198057625198.4
2.73-30.1416.8192477372198.4
3-3.430.08510.2193557431198.4
3.43-4.320.05415.4195937504198.2
4.32-28.760.04418.5197027493197.4

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→28.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.153 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.157
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 4. ENDOGENOUS COFACTOR FMN WAS FOUND BOUND TO THE PROTEIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1974 5 %RANDOM
Rwork0.169 ---
obs0.171 39318 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.02 Å2 / Biso mean: 27.7 Å2 / Biso min: 10.74 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å20 Å2
2---1.59 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 1.99→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 62 364 4398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224148
X-RAY DIFFRACTIONr_bond_other_d0.0020.022803
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9955639
X-RAY DIFFRACTIONr_angle_other_deg0.98936860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7375502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1524.49196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13815733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.91526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024537
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02807
X-RAY DIFFRACTIONr_nbd_refined0.2080.2955
X-RAY DIFFRACTIONr_nbd_other0.2050.23204
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22100
X-RAY DIFFRACTIONr_nbtor_other0.0890.22221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2361
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0780.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.29
X-RAY DIFFRACTIONr_mcbond_it2.21132667
X-RAY DIFFRACTIONr_mcbond_other0.5843986
X-RAY DIFFRACTIONr_mcangle_it2.94154064
X-RAY DIFFRACTIONr_scbond_it5.68781878
X-RAY DIFFRACTIONr_scangle_it7.282111570
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3302 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.225
LOOSE THERMAL1.8310
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 127 -
Rwork0.244 2666 -
all-2793 -
obs--96.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.253-0.0960.03340.79390.16280.61260.00760.05990.0431-0.07690.0043-0.04380.02740.0279-0.012-0.0438-0.0163-0.0087-0.02060.0154-0.047828.51225.1039.363
20.2114-0.11520.06860.70860.08130.3301-0.00760.01080.00790.12-0.01030.07030.0502-0.06410.0179-0.0226-0.01580.0077-0.02580.0005-0.033817.99231.596421.4583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 247
2X-RAY DIFFRACTION2B2 - 247

+
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