[English] 日本語
Yorodumi
- PDB-3nwz: Crystal Structure of BH2602 protein from Bacillus halodurans with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nwz
TitleCrystal Structure of BH2602 protein from Bacillus halodurans with CoA, Northeast Structural Genomics Consortium Target BhR199
ComponentsBH2602 protein
KeywordsStructural Genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / cytosol
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / BH2602 protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.566 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target BhR199
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BH2602 protein
B: BH2602 protein
C: BH2602 protein
D: BH2602 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4357
Polymers80,4754
Non-polymers9603
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-83 kcal/mol
Surface area26000 Å2
MethodPISA
2
A: BH2602 protein
C: BH2602 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1014
Polymers40,2372
Non-polymers8642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-39 kcal/mol
Surface area15640 Å2
MethodPISA
3
B: BH2602 protein
D: BH2602 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3343
Polymers40,2372
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-36 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.243, 89.733, 71.850
Angle α, β, γ (deg.)90.00, 107.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
BH2602 protein


Mass: 20118.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH2602 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9K9P3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.2M ammonium sulfate, 0.1M hepes, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2010 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 38995 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 48.09 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18

-
Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.566→27.883 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 31.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1022 5.1 %
Rwork0.2309 --
obs0.2326 20053 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.564 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.2745 Å20 Å2-22.7357 Å2
2---20.9524 Å2-0 Å2
3---12.6778 Å2
Refinement stepCycle: LAST / Resolution: 2.566→27.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4607 0 58 16 4681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094725
X-RAY DIFFRACTIONf_angle_d1.3316392
X-RAY DIFFRACTIONf_dihedral_angle_d19.4991806
X-RAY DIFFRACTIONf_chiral_restr0.097743
X-RAY DIFFRACTIONf_plane_restr0.007823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5662-2.70140.39811280.3042517X-RAY DIFFRACTION91
2.7014-2.87050.3621460.27442753X-RAY DIFFRACTION100
2.8705-3.09180.30691640.26822694X-RAY DIFFRACTION100
3.0918-3.40250.31771420.2432751X-RAY DIFFRACTION100
3.4025-3.89370.25661390.21952767X-RAY DIFFRACTION100
3.8937-4.90130.20341370.17622770X-RAY DIFFRACTION100
4.9013-27.88430.20581660.21832779X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 28.2716 Å / Origin y: 34.0439 Å / Origin z: 33.6898 Å
111213212223313233
T0.0734 Å2-0.0042 Å2-0.0125 Å2-0.1122 Å20.0106 Å2--0.1518 Å2
L0.0029 °2-0.4697 °20.0076 °2-0.9665 °20.1733 °2--0.5417 °2
S0.0442 Å °0.0031 Å °-0.0888 Å °-0.0927 Å °-0.062 Å °0.3107 Å °-0.0117 Å °0.0198 Å °0.0018 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