[English] 日本語
Yorodumi
- PDB-3dto: Crystal structure of the metal-dependent HD domain-containing hyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dto
TitleCrystal structure of the metal-dependent HD domain-containing hydrolase BH2835 from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR130.
ComponentsBH2835 protein
Keywordsstructural genomics / unknown function / all alpha-helical protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


HD-domain/PDEase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1910 / HD domain / HD domain / Cyclin A; domain 1 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsForouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Wang, D. ...Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Wang, D. / Tong, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the metal-dependent HD domain-containing hydrolase BH2835 from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR130.
Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Wang, D. / Tong, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BH2835 protein
B: BH2835 protein
C: BH2835 protein
D: BH2835 protein


Theoretical massNumber of molelcules
Total (without water)104,8164
Polymers104,8164
Non-polymers00
Water00
1
A: BH2835 protein
B: BH2835 protein


Theoretical massNumber of molelcules
Total (without water)52,4082
Polymers52,4082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area20210 Å2
MethodPISA
2
C: BH2835 protein
D: BH2835 protein


Theoretical massNumber of molelcules
Total (without water)52,4082
Polymers52,4082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.564, 47.987, 111.159
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
BH2835 protein


Mass: 26204.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2835 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9K916

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 0.1M mops (pH 7), 80% PEG 400, and 0.1M potassium acetate. , microbatch under oil, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2007 / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 22713 / % possible obs: 74.5 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 3.4 % / Biso Wilson estimate: 74.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.075 / Net I/σ(I): 13.1
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 3 / Rsym value: 0.185 / % possible all: 58.4

-
Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→19.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 335033.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2147 9.5 %RANDOM
Rwork0.248 ---
obs0.248 22713 76.3 %-
all-15076 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1144 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 70.3 Å2
Baniso -1Baniso -2Baniso -3
1-21.68 Å20 Å21.82 Å2
2---2.83 Å20 Å2
3----18.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 0 0 6132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.32 136 10.3 %
Rwork0.286 1190 -
obs--43.4 %

+
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://pdbjlvh1.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