[English] 日本語
Yorodumi
- PDB-6a6q: Crystal structure of a lignin peroxidase isozyme H8 variant that ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a6q
TitleCrystal structure of a lignin peroxidase isozyme H8 variant that is stable at very acidic pH
ComponentsLigninase H8
KeywordsOXIDOREDUCTASE / peroxidase / heme binding domain
Function / homology
Function and homology information


lignin peroxidase / diarylpropane peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site ...Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME B/C / Ligninase H8
Similarity search - Component
Biological speciesPhanerochaete chrysosporium RP-78 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsSeo, H. / Kim, K.-J. / Pham, L.T.M.
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: In silico-designed lignin peroxidase fromPhanerochaete chrysosporiumshows enhanced acid stability for depolymerization of lignin.
Authors: Pham, L.T.M. / Seo, H. / Kim, K.J. / Kim, Y.H.
History
DepositionJun 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Derived calculations / Structure summary
Category: pdbx_struct_conn_angle / struct ...pdbx_struct_conn_angle / struct / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn_type.id
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ligninase H8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6507
Polymers37,6751
Non-polymers9756
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-22 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.212, 99.621, 48.322
Angle α, β, γ (deg.)90.000, 113.860, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ligninase H8 / Diarylpropane peroxidase / Lignin peroxidase


Mass: 37674.926 Da / Num. of mol.: 1 / Mutation: A55R, N156E, H239E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium RP-78 (fungus)
Gene: LPOA / Plasmid: pET21b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06181, lignin peroxidase
#2: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2018
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 40502 / % possible obs: 97.7 % / Redundancy: 3.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.049 / Rrim(I) all: 0.093 / Net I/σ(I): 32.06
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 1927 / CC1/2: 0.803 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b80

1b80


Resolution: 1.67→29.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.555 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1707 1982 4.9 %RANDOM
Rwork0.1415 ---
obs0.1429 38505 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.38 Å2 / Biso mean: 21.237 Å2 / Biso min: 11.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å21.01 Å2
2---1.29 Å20 Å2
3----0.93 Å2
Refinement stepCycle: final / Resolution: 1.67→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 63 249 2917
Biso mean--20.35 31.58 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0142793
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172416
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.6973824
X-RAY DIFFRACTIONr_angle_other_deg1.1381.6665693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86924.148135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54715407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4211511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023215
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02512
LS refinement shellResolution: 1.666→1.709 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 128 -
Rwork0.197 2613 -
all-2741 -
obs--88.94 %

+
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