[English] 日本語
Yorodumi
- PDB-3djb: Crystal structure of a HD-superfamily hydrolase (BT9727_1981) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3djb
TitleCrystal structure of a HD-superfamily hydrolase (BT9727_1981) from Bacillus thuringiensis, Northeast Structural Genomics Consortium Target BuR114
ComponentsHydrolase, HD family
KeywordsHYDROLASE / all alpha-helical protein. / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
HD-domain/PDEase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1910 / HD domain profile. / 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 ...HD-domain/PDEase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1910 / HD domain profile. / 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
Hydrolase, HD family
Similarity search - Component
Biological speciesBacillus thuringiensis serovar konkukian (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsForouhar, F. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Maglaqui, M. / Owen, L.A. ...Forouhar, F. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Maglaqui, M. / Owen, L.A. / Wang, D. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a HD-superfamily hydrolase (BT9727_1981) from Bacillus thuringiensis, Northeast Structural Genomics Consortium Target BuR114
Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Maglaqui, M. / Owen, L.A. / Wang, D. / Baran, M.C. / Liu, J. / Acton, T.B. / ...Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Maglaqui, M. / Owen, L.A. / Wang, D. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydrolase, HD family
B: Hydrolase, HD family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8884
Polymers52,8392
Non-polymers492
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-24 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.273, 66.273, 101.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Hydrolase, HD family


Mass: 26419.447 Da / Num. of mol.: 2 / Mutation: E31R, L36M, I117L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar konkukian (bacteria)
Strain: 97-27 / Gene: BT9727_1981 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6HJG6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM NaCl, and 5 mM DTT. Reservoir solution: 100 mM Hepes (pH 7.5), 40% PEG 1k, and 100 mM KNO3., microbatch under oil, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2007 / 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: 2.9→30 Å / Num. all: 19157 / Num. obs: 18813 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.056 / Net I/σ(I): 24.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1939 / Rsym value: 0.351 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→19.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 568553.53 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1493 9.4 %RANDOM
Rwork0.246 ---
all0.247 19078 --
obs0.246 15854 83.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.1085 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 71.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 2 12 3060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4 122 11.3 %
Rwork0.374 961 -
obs-961 57.2 %

+
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