[English] 日本語
Yorodumi
- PDB-3tbb: Small laccase from Streptomyces viridosporus T7A; alternate cryst... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tbb
TitleSmall laccase from Streptomyces viridosporus T7A; alternate crystal form.
Componentssmall laccase, oxidoreductase
KeywordsOXIDOREDUCTASE / two-domain laccase / secreted
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN MOLECULE / PHOSPHATE ION / Small laccase, multi-copper oxidase
Similarity search - Component
Biological speciesStreptomyces viridosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLukk, T. / Majumdar, S. / Gerlt, J.A. / Nair, S.K.
CitationJournal: Biochemistry / Year: 2014
Title: Roles of small laccases from Streptomyces in lignin degradation.
Authors: Majumdar, S. / Lukk, T. / Solbiati, J.O. / Bauer, S. / Nair, S.K. / Cronan, J.E. / Gerlt, J.A.
History
DepositionAug 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: small laccase, oxidoreductase
B: small laccase, oxidoreductase
C: small laccase, oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,16225
Polymers102,6393
Non-polymers1,52322
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-196 kcal/mol
Surface area27830 Å2
MethodPISA
2
A: small laccase, oxidoreductase
B: small laccase, oxidoreductase
C: small laccase, oxidoreductase
hetero molecules

A: small laccase, oxidoreductase
B: small laccase, oxidoreductase
C: small laccase, oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,32550
Polymers205,2786
Non-polymers3,04744
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area31480 Å2
ΔGint-421 kcal/mol
Surface area51860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.000, 127.000, 155.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsDetermined via gel-filtration chromatography.

-
Components

#1: Protein small laccase, oxidoreductase


Mass: 34212.988 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridosporus (bacteria) / Strain: T7A / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: J9PBR2*PLUS, laccase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein concentrationw as 20 mg/ml in Tris-HCl (pH 7.9); the precipitant contained 5% 2-propanol, and 2.5 M dibasic potassium phosphate/monobasic sodium phosphate (pH 5.5)., VAPOR DIFFUSION, ...Details: Protein concentrationw as 20 mg/ml in Tris-HCl (pH 7.9); the precipitant contained 5% 2-propanol, and 2.5 M dibasic potassium phosphate/monobasic sodium phosphate (pH 5.5)., VAPOR DIFFUSION, HANGING DROP, temperature 282K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 20, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 64712 / Num. obs: 64657 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.195 Å2 / Rmerge(I) obs: 0.214 / Net I/σ(I): 15.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.380.0172.239230462191100
2.38-2.480.0172.559986267011100
2.48-2.590.0173.319337162631100
2.59-2.730.0174.479705165121100
2.73-2.90.0176.429510263801100
2.9-3.120.0179.839419463231100
3.12-3.430.01715.89548064201100
3.43-3.930.01724.749675665461100
3.93-4.930.01736.849493364581100
4.93-300.01742.78962506835199.3

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_764refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TAS

3tas


Resolution: 2.3→29.931 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.8789 / SU ML: 0.59 / σ(F): 1.99 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 3232 5 %random
Rwork0.161 ---
all0.182 64712 --
obs0.1632 64597 99.96 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.296 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 84.17 Å2 / Biso mean: 32.367 Å2 / Biso min: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.0349 Å2-0 Å20 Å2
2--0.0349 Å2-0 Å2
3----0.0699 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6421 0 53 563 7037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086672
X-RAY DIFFRACTIONf_angle_d1.3429061
X-RAY DIFFRACTIONf_chiral_restr0.112926
X-RAY DIFFRACTIONf_plane_restr0.0081198
X-RAY DIFFRACTIONf_dihedral_angle_d13.1462386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.33440.2561390.234726332772100
2.3344-2.37090.27491370.228526182755100
2.3709-2.40970.30331400.232426452785100
2.4097-2.45120.291390.240926542793100
2.4512-2.49580.29521390.233326312770100
2.4958-2.54380.25621400.214626502790100
2.5438-2.59570.23261380.193826362774100
2.5957-2.65210.24441390.193726342773100
2.6521-2.71370.24231400.182826602800100
2.7137-2.78150.23911390.186126482787100
2.7815-2.85670.24761400.178426492789100
2.8567-2.94070.22891400.170626612801100
2.9407-3.03550.18771400.160326582798100
3.0355-3.14390.19591390.150826352774100
3.1439-3.26960.17141410.152726792820100
3.2696-3.41820.20251400.145426602800100
3.4182-3.59820.20161400.145826652805100
3.5982-3.82320.22151410.147926722813100
3.8232-4.11770.1721420.131326902832100
4.1177-4.53080.14931430.113227142857100
4.5308-5.18350.17261410.112826922833100
5.1835-6.51950.15641440.139427472891100
6.5195-29.93330.21551510.20272834298599

+
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