[English] 日本語
Yorodumi
- PDB-4f6a: High-resolution x-ray Structure of the tetramutant of BH1408 prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f6a
TitleHigh-resolution x-ray Structure of the tetramutant of BH1408 protein from Bacillus halodurans, Northeast Structural Genomics Consortium (NESG) Target BhR182
ComponentsBH1408 protein
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / BH1408
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / BH1408 protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.009 Å
AuthorsKuzin, A. / Neely, H. / Odukwe, N. / Seetharaman, J. / Patel, P. / Xiao, R. / Kohan, E. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Neely, H. / Odukwe, N. / Seetharaman, J. / Patel, P. / Xiao, R. / Kohan, E. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target BhR182
Authors: Kuzin, A. / Neely, H. / Odukwe, N. / Seetharaman, J. / Patel, P. / Xiao, R. / Kohan, E. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BH1408 protein
B: BH1408 protein


Theoretical massNumber of molelcules
Total (without water)36,3624
Polymers36,3622
Non-polymers02
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-29 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.842, 86.842, 163.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsdimer,39.71 kD,98.6%

-
Components

#1: Protein BH1408 protein


Mass: 18181.127 Da / Num. of mol.: 2 / Mutation: E12Y, F44R, D134E, A138R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: BH1408 / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9KD11
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M KSCN, 0.1M TAPS, 20% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 5, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 46521 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 33.1

-
Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4E0A

4e0a


Resolution: 2.009→34.174 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.18 / σ(F): 1.38 / Phase error: 21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 2350 5.05 %
Rwork0.1914 --
obs0.1928 46513 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.095 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0575 Å2-0 Å20 Å2
2--4.0575 Å20 Å2
3----8.115 Å2
Refinement stepCycle: LAST / Resolution: 2.009→34.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 22 328 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082589
X-RAY DIFFRACTIONf_angle_d1.0023496
X-RAY DIFFRACTIONf_dihedral_angle_d15.22988
X-RAY DIFFRACTIONf_chiral_restr0.068388
X-RAY DIFFRACTIONf_plane_restr0.004457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0091-2.05010.27991050.23441934X-RAY DIFFRACTION73
2.0501-2.09470.20681150.19932465X-RAY DIFFRACTION92
2.0947-2.14340.21791300.18132458X-RAY DIFFRACTION93
2.1434-2.1970.20891400.19372511X-RAY DIFFRACTION94
2.197-2.25640.23071460.20632522X-RAY DIFFRACTION94
2.2564-2.32280.22981290.19672590X-RAY DIFFRACTION97
2.3228-2.39770.2161190.17592629X-RAY DIFFRACTION97
2.3977-2.48340.22141490.18552641X-RAY DIFFRACTION99
2.4834-2.58280.22951350.19252655X-RAY DIFFRACTION99
2.5828-2.70030.2371470.20092655X-RAY DIFFRACTION99
2.7003-2.84260.25461430.21622671X-RAY DIFFRACTION99
2.8426-3.02060.25561540.21712663X-RAY DIFFRACTION99
3.0206-3.25370.24821550.20872693X-RAY DIFFRACTION100
3.2537-3.58080.21931460.19922720X-RAY DIFFRACTION99
3.5808-4.09820.17851430.17812730X-RAY DIFFRACTION100
4.0982-5.16040.17191420.15052779X-RAY DIFFRACTION100
5.1604-34.17930.26031520.20982847X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -42.8475 Å / Origin y: 0.4672 Å / Origin z: 14.309 Å
111213212223313233
T0.2049 Å2-0.0068 Å20.0007 Å2-0.2793 Å20.0028 Å2--0.1707 Å2
L0.7477 °20.8063 °20.109 °2-2.3075 °20.168 °2--0.7225 °2
S0.0401 Å °-0.1319 Å °-0.0058 Å °0.0027 Å °-0.0759 Å °-0.0387 Å °0.0016 Å °0.0051 Å °0.0362 Å °
Refinement TLS groupSelection details: all

+
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