[English] 日本語
Yorodumi
- PDB-2hag: Crystal structure of a putative dyp-type peroxidase protein (so_0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hag
TitleCrystal structure of a putative dyp-type peroxidase protein (so_0740) from shewanella oneidensis at 2.75 A resolution
ComponentsMelanin biosynthesis protein TyrA, putative
KeywordsHYDROLASE / Ferredoxin-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
Dyp-type heme-dependent peroxidase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.
Authors: Zubieta, C. / Krishna, S.S. / Kapoor, M. / Kozbial, P. / McMullan, D. / Axelrod, H.L. / Miller, M.D. / Abdubek, P. / Ambing, E. / Astakhova, T. / Carlton, D. / Chiu, H.J. / Clayton, T. / ...Authors: Zubieta, C. / Krishna, S.S. / Kapoor, M. / Kozbial, P. / McMullan, D. / Axelrod, H.L. / Miller, M.D. / Abdubek, P. / Ambing, E. / Astakhova, T. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kumar, A. / Marciano, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Reyes, R. / Rife, C.L. / Schimmel, P. / van den Bedem, H. / Weekes, D. / White, A. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Melanin biosynthesis protein TyrA, putative


Theoretical massNumber of molelcules
Total (without water)36,4701
Polymers36,4701
Non-polymers00
Water86548
1
A: Melanin biosynthesis protein TyrA, putative

A: Melanin biosynthesis protein TyrA, putative


Theoretical massNumber of molelcules
Total (without water)72,9402
Polymers72,9402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)94.310, 94.310, 113.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Melanin biosynthesis protein TyrA, putative


Mass: 36469.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: np_716371.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EIU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.66 %
Description: AFTER THE INITIAL TRACE, A MODEL OF A HOMOLOGOUS PROTEIN (PDB ENTRY 2GVK) WAS USED TO FACILITATE COMPLETION OF THE MODEL.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 5.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979291, 0.918370, 0.978940
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792911
20.918371
30.978941
ReflectionResolution: 2.75→29.54 Å / Num. obs: 13932 / % possible obs: 95.4 % / Biso Wilson estimate: 58.902 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.75-2.850.8351.78805229786.7
2.85-2.960.6712.28529221489.8
2.96-3.10.5432.79500245992.1
3.1-3.260.43.69309241594.5
3.26-3.460.2665.39345242396.8
3.46-3.730.1528.59908257398.4
3.73-4.10.08313.99809254299.3
4.1-4.690.05618.69839255999.3
4.690.05719.19792256999.6

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.75→29.54 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 22.648 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.279
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING DUE TO PARTIAL S-MET INCORPORATION. 3. ADDITIONAL ELECTRON DENSITY WAS NOTED ADJACENT TO RESIDUE A20 BUT NOT MODELLED. 4. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 691 5 %RANDOM
Rwork0.191 ---
obs0.193 13888 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.485 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20 Å2
2---2 Å20 Å2
3---3.99 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 0 48 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222513
X-RAY DIFFRACTIONr_bond_other_d0.0010.022179
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9473394
X-RAY DIFFRACTIONr_angle_other_deg0.61535081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0424.361133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82415424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4041515
X-RAY DIFFRACTIONr_chiral_restr0.0630.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
X-RAY DIFFRACTIONr_nbd_refined0.2280.3600
X-RAY DIFFRACTIONr_nbd_other0.2120.32312
X-RAY DIFFRACTIONr_nbtor_refined0.1980.51241
X-RAY DIFFRACTIONr_nbtor_other0.0930.51414
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.5130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.58
X-RAY DIFFRACTIONr_mcbond_it2.6731578
X-RAY DIFFRACTIONr_mcbond_other0.5323622
X-RAY DIFFRACTIONr_mcangle_it3.80352452
X-RAY DIFFRACTIONr_scbond_it2.57431064
X-RAY DIFFRACTIONr_scangle_it3.7615942
LS refinement shellResolution: 2.749→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 54 -
Rwork0.34 953 -
obs-1007 99.11 %
Refinement TLS params.Method: refined / Origin x: 27.641 Å / Origin y: 27.514 Å / Origin z: 38.523 Å
111213212223313233
T-0.0295 Å2-0.0812 Å20.0601 Å2--0.0528 Å20.0299 Å2---0.2081 Å2
L1.306 °2-0.3974 °2-0.1321 °2-2.2233 °2-0.2717 °2--2.4529 °2
S0.0486 Å °0.3797 Å °0.1498 Å °-0.3947 Å °-0.1279 Å °-0.1833 Å °-0.0518 Å °0.1326 Å °0.0794 Å °
Refinement TLS groupSelection: 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