[English] 日本語
Yorodumi
- PDB-5zcw: Structure of the Methanosarcina mazei class II CPD-photolyase in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zcw
TitleStructure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion
Components
  • 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'
  • 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'
  • Deoxyribodipyrimidine photolyase
KeywordsDNA BINDING PROTEIN/DNA / DNA repair / photorepair / CPD / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / DNA repair / nucleotide binding / DNA binding
Similarity search - Function
DNA photolyase class 2 / : / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily ...DNA photolyase class 2 / : / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / DNA / DNA (> 10) / Deoxyribodipyrimidine photo-lyase / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMaestre-Reyna, M. / Bessho, Y.
CitationJournal: IUCrJ / Year: 2018
Title: Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA.
Authors: Maestre-Reyna, M. / Yamamoto, J. / Huang, W.C. / Tsai, M.D. / Essen, L.O. / Bessho, Y.
History
DepositionFeb 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyribodipyrimidine photolyase
B: Deoxyribodipyrimidine photolyase
C: 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'
D: 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'
E: 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'
F: 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,72510
Polymers127,9996
Non-polymers1,7264
Water6,089338
1
A: Deoxyribodipyrimidine photolyase
C: 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'
D: 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9406
Polymers63,9993
Non-polymers9413
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-39 kcal/mol
Surface area21590 Å2
MethodPISA
2
B: Deoxyribodipyrimidine photolyase
E: 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'
F: 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7854
Polymers63,9993
Non-polymers7861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-20 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.100, 114.420, 166.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 462 / Label seq-ID: 21 - 480

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Deoxyribodipyrimidine photolyase


Mass: 55123.480 Da / Num. of mol.: 2 / Mutation: M377T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F8I5V2, UniProt: Q8PYK9*PLUS

-
DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'


Mass: 4569.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'


Mass: 4305.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 342 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M NaOAc pH 4.6, 0.25 M (NH4)2SO4, 4% PEG 4000

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC TPS 05A11
SYNCHROTRONSPring-8 BL32XU21
Detector
TypeIDDetectorDateDetails
RAYONIX MX300-HS1CCDAug 16, 2017
RAYONIX MX-2252CCDJul 19, 2017K-B mirrors fabricated with EEM (Elastic Emission Machining) technique (Osaka mirror)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2-Cooled Fixed-Exit Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2liquid nitrogen cooled double crystal Si (111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 2.7→94.29 Å / Num. obs: 38064 / % possible obs: 99.89 % / Redundancy: 6.8 % / CC1/2: 0.857 / Rmerge(I) obs: 0.5437 / Rpim(I) all: 0.2219 / Net I/σ(I): 10.67
Reflection shellResolution: 2.7→2.796 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 3734 / CC1/2: 0.522 / Rpim(I) all: 0.5563 / % possible all: 99.87

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSJune 1, 2017data reduction
XSCALEJune 1, 2017data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XRZ

2xrz


Resolution: 2.7→94.29 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.881 / SU B: 28.858 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.997 / ESU R Free: 0.339 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25726 1883 4.9 %RANDOM
Rwork0.21397 ---
obs0.2161 36183 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.107 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--1.92 Å2-0 Å2
3----2.78 Å2
Refinement stepCycle: 1 / Resolution: 2.7→94.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6855 979 115 342 8291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0188308
X-RAY DIFFRACTIONr_bond_other_d0.0020.026751
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.86911518
X-RAY DIFFRACTIONr_angle_other_deg1.064315635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6865892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43523.611324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.751151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7291541
X-RAY DIFFRACTIONr_chiral_restr0.0980.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218737
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021830
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.663.2413560
X-RAY DIFFRACTIONr_mcbond_other0.6593.2383558
X-RAY DIFFRACTIONr_mcangle_it1.1524.8534445
X-RAY DIFFRACTIONr_mcangle_other1.1524.8544446
X-RAY DIFFRACTIONr_scbond_it0.6413.3394748
X-RAY DIFFRACTIONr_scbond_other0.6413.344749
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0525.0117067
X-RAY DIFFRACTIONr_long_range_B_refined3.92962.85217560
X-RAY DIFFRACTIONr_long_range_B_other3.89762.81817527
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 26566 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 140 -
Rwork0.33 2628 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.42750.49270.14922.0998-0.02081.9756-0.00940.6647-0.5558-0.55970.1058-0.00550.2011-0.1229-0.09650.2956-0.0119-0.00720.2049-0.10150.400916.291-27.782-20.345
21.9301-0.13860.0372.3173-0.03071.89370.04630.0074-0.09260.08260.018-0.1737-0.2597-0.0278-0.06440.1497-0.00370.0190.00350.01670.181222.08-12.098-1.34
33.14852.38780.8743.44351.35333.29070.26810.0040.23390.46510.02320.1027-0.71350.2608-0.29121.3291-0.09950.15790.18950.05910.511732.42728.31-9.782
41.96931.7378-0.5063.74710.29652.4347-0.13460.63530.1821-0.36630.4712-0.1797-0.6570.1161-0.33650.7405-0.07230.06360.48280.10420.26226.60612.435-30.11
54.9507-0.1921.07213.55660.77823.65520.0444-0.791-0.3250.78110.11720.7080.0256-0.6861-0.16160.42910.00740.09440.5690.05290.4903-0.035-5.17210.085
65.8071-2.3433-2.62083.41343.512310.88240.33910.51240.6476-0.0705-0.24920.3799-0.5688-1.1551-0.08990.83250.0304-0.04780.82940.1460.58439.3211.284-45.316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 186
2X-RAY DIFFRACTION2A198 - 462
3X-RAY DIFFRACTION2A502
4X-RAY DIFFRACTION3B3 - 187
5X-RAY DIFFRACTION4B221 - 462
6X-RAY DIFFRACTION4B501
7X-RAY DIFFRACTION5C1 - 13
8X-RAY DIFFRACTION5D1 - 14
9X-RAY DIFFRACTION6E5 - 13
10X-RAY DIFFRACTION6F1 - 11

+
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