[English] 日本語
Yorodumi
- PDB-3nqk: Crystal structure of a STRUCTURAL GENOMICS, UNKNOWN FUNCTION (BAC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nqk
TitleCrystal structure of a STRUCTURAL GENOMICS, UNKNOWN FUNCTION (BACOVA_03322) from Bacteroides ovatus at 2.61 A resolution
Componentsuncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Uncharacterised protein PF14274, DUF4361 / Domain of unknown function DUF4361 / Domain of unknown function DUF4973 / BT_3044-like, C-terminal / Domain of unknown function (DUF4973) / hypothetical protein (bacova_03559) / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like ...Uncharacterised protein PF14274, DUF4361 / Domain of unknown function DUF4361 / Domain of unknown function DUF4973 / BT_3044-like, C-terminal / Domain of unknown function (DUF4973) / hypothetical protein (bacova_03559) / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DUF4973 domain-containing protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a STRUCTURAL GENOMICS, UNKNOWN FUNCTION (BACOVA_03322) from Bacteroides ovatus at 2.61 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 1.5Nov 27, 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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5753
Polymers37,4511
Non-polymers1242
Water1,42379
1
A: uncharacterized protein
hetero molecules

A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1506
Polymers74,9022
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area3010 Å2
ΔGint-7 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.073, 124.073, 66.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

-
Components

#1: Protein uncharacterized protein


Mass: 37451.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_03322 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LZP6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (22-339) WAS EXPRESSED WITH A N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...THE CONSTRUCT (22-339) WAS EXPRESSED WITH A N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 22 TO 339 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.200000000M (NH4)2Tartrate, 20.000000000% PEG-3350, No Buffer pH 6.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97937,0.97908
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2010 / 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
20.979371
30.979081
ReflectionResolution: 2.61→29.801 Å / Num. obs: 18340 / % possible obs: 99.9 % / Redundancy: 11.7 % / Rsym value: 0.158

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.61→29.801 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 16.365 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.241
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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. (4). WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. (5). ETHYLENE GLYCOL (EDO), USED AS A CRYOPROTECTANT, WAS MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 940 5.1 %RANDOM
Rwork0.198 ---
obs0.2 18334 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.73 Å2 / Biso mean: 51.264 Å2 / Biso min: 21.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å20 Å2
2--0.83 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 8 79 2544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222540
X-RAY DIFFRACTIONr_bond_other_d0.0010.021700
X-RAY DIFFRACTIONr_angle_refined_deg0.9171.9593448
X-RAY DIFFRACTIONr_angle_other_deg0.61634149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.145309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.49424.8125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66415434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6881512
X-RAY DIFFRACTIONr_chiral_restr0.0640.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
X-RAY DIFFRACTIONr_mcbond_it1.86831530
X-RAY DIFFRACTIONr_mcbond_other0.3253615
X-RAY DIFFRACTIONr_mcangle_it3.57852496
X-RAY DIFFRACTIONr_scbond_it5.2881010
X-RAY DIFFRACTIONr_scangle_it8.11411949
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 81 -
Rwork0.387 1260 -
all-1341 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: 44.637 Å / Origin y: 21.369 Å / Origin z: 31.048 Å
111213212223313233
T0.1176 Å2-0.0096 Å2-0.0452 Å2-0.1519 Å20.0325 Å2--0.1676 Å2
L0.5417 °2-0.0767 °2-0.3697 °2-1.4368 °2-0.4912 °2--1.0519 °2
S-0.0248 Å °-0.0402 Å °-0.0101 Å °0.1184 Å °0.1046 Å °0.1861 Å °0.0158 Å °-0.0368 Å °-0.0797 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