[English] 日本語
Yorodumi
- PDB-6dk9: Yeast Ddi2 Cyanamide Hydratase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dk9
TitleYeast Ddi2 Cyanamide Hydratase
ComponentsDNA damage-inducible protein
KeywordsLYASE / Zn-metalloprotein / HD-domain / hydratase / cyanamide / METAL BINDING PROTEIN
Function / homologyCyanamide hydratase / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / metal ion binding / DNA damage-inducible protein
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMoore, S.A. / Xiao, W. / Li, J.
Funding support Canada, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-04580 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2011-262138 Canada
Canadian Institutes of Health Research (CIHR)MOP-126155 Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure of Ddi2, a highly inducible detoxifying metalloenzyme fromSaccharomyces cerevisiae.
Authors: Li, J. / Jia, Y. / Lin, A. / Hanna, M. / Chelico, L. / Xiao, W. / Moore, S.A.
History
DepositionMay 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA damage-inducible protein
B: DNA damage-inducible protein
C: DNA damage-inducible protein
D: DNA damage-inducible protein
E: DNA damage-inducible protein
F: DNA damage-inducible protein
G: DNA damage-inducible protein
H: DNA damage-inducible protein
I: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,99446
Polymers234,7159
Non-polymers3,27837
Water5,873326
1
A: DNA damage-inducible protein
hetero molecules

A: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,86610
Polymers52,1592
Non-polymers7078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area4130 Å2
ΔGint-190 kcal/mol
Surface area17650 Å2
MethodPISA
2
B: DNA damage-inducible protein
C: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,05812
Polymers52,1592
Non-polymers89910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-215 kcal/mol
Surface area17620 Å2
MethodPISA
3
D: DNA damage-inducible protein
E: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,44216
Polymers52,1592
Non-polymers1,28414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-266 kcal/mol
Surface area18090 Å2
MethodPISA
4
F: DNA damage-inducible protein
G: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7709
Polymers52,1592
Non-polymers6117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-165 kcal/mol
Surface area17960 Å2
MethodPISA
5
H: DNA damage-inducible protein
I: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2904
Polymers52,1592
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-93 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.456, 264.456, 119.152
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein
DNA damage-inducible protein


Mass: 26079.455 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: SCY_1694 / Plasmid: PGEX-6P1 / Details (production host): GST-fusion protein / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7A1Y4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 76 % / Description: flattened discs
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.1-1.3 M Ammonium Sulfate 0.2 M Arginine 0.1 M N-morpholino ethane sulfonate pH 5.6
PH range: 5.2-6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.12713 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 15, 2014 / Details: Toroidal focusing mirrors
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.6→39.7 Å / Num. obs: 144816 / % possible obs: 99 % / Redundancy: 7.7 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7127 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→39.7 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.09
Details: Iterative Maximum Likelihood refinement in PHENIX and model building with Coot. The authors state that Although Chains H and I are included in the model structure, in general these chains ...Details: Iterative Maximum Likelihood refinement in PHENIX and model building with Coot. The authors state that Although Chains H and I are included in the model structure, in general these chains are considered unreliable due to high B-factors and poor electron density. These chains should not be used for any structural analysis.
RfactorNum. reflection% reflection
Rfree0.2168 7189 4.97 %
Rwork0.2006 --
obs0.2014 144610 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16138 0 149 326 16613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416669
X-RAY DIFFRACTIONf_angle_d0.81222796
X-RAY DIFFRACTIONf_dihedral_angle_d11.6319843
X-RAY DIFFRACTIONf_chiral_restr0.0472624
X-RAY DIFFRACTIONf_plane_restr0.0062928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62960.28951920.26054247X-RAY DIFFRACTION92
2.6296-2.66050.28682410.24924531X-RAY DIFFRACTION98
2.6605-2.6930.2742220.22874519X-RAY DIFFRACTION98
2.693-2.7270.2542440.23294493X-RAY DIFFRACTION98
2.727-2.76290.27672390.24974576X-RAY DIFFRACTION99
2.7629-2.80070.26622240.24324523X-RAY DIFFRACTION99
2.8007-2.84080.26172600.22724541X-RAY DIFFRACTION98
2.8408-2.88310.2772440.22744524X-RAY DIFFRACTION99
2.8831-2.92820.26312270.22664592X-RAY DIFFRACTION99
2.9282-2.97620.25492560.22324543X-RAY DIFFRACTION99
2.9762-3.02750.29222430.28414491X-RAY DIFFRACTION98
3.0275-3.08250.33152210.31154545X-RAY DIFFRACTION98
3.0825-3.14180.24432340.2274594X-RAY DIFFRACTION99
3.1418-3.20590.22872500.21614574X-RAY DIFFRACTION99
3.2059-3.27550.25832300.22484576X-RAY DIFFRACTION99
3.2755-3.35170.23432760.22974573X-RAY DIFFRACTION99
3.3517-3.43550.2572410.21344593X-RAY DIFFRACTION100
3.4355-3.52830.25012450.20734645X-RAY DIFFRACTION100
3.5283-3.63210.20612460.19834609X-RAY DIFFRACTION100
3.6321-3.74920.22292330.1964606X-RAY DIFFRACTION100
3.7492-3.88310.20022140.18234656X-RAY DIFFRACTION100
3.8831-4.03840.20242190.1784687X-RAY DIFFRACTION100
4.0384-4.2220.18412250.15964650X-RAY DIFFRACTION100
4.222-4.44440.15582310.14754678X-RAY DIFFRACTION100
4.4444-4.72240.16322310.14984644X-RAY DIFFRACTION100
4.7224-5.08630.16152470.16634656X-RAY DIFFRACTION100
5.0863-5.59690.21172410.1884622X-RAY DIFFRACTION99
5.5969-6.40390.20392430.20384652X-RAY DIFFRACTION99
6.4039-8.05720.20952960.20434636X-RAY DIFFRACTION99
8.0572-39.72190.18272740.1934645X-RAY DIFFRACTION97
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)
10.6583-0.15150.241.1083-0.172.4274-0.0471-0.10680.084-0.0015-0.04750.1074-0.2228-0.50730.09410.37640.2075-0.02050.7265-0.01380.359535.158385.7533127.4308
20.5226-0.075-0.30161.5491-0.08771.3129-0.0684-0.1416-0.00780.1660.09830.1353-0.2789-0.3563-0.01610.36870.225-0.00520.65830.02880.421.0595105.340795.6383
30.81750.0323-0.2311.0669-0.25752.0242-0.0481-0.0789-0.0517-0.03180.05080.05360.0516-0.0518-0.00480.26520.1071-0.03420.4170.01670.343139.475789.117978.4873
40.58560.1184-0.00191.18650.03071.086-0.0023-0.08510.01160.12310.02180.0476-0.1265-0.0989-0.0090.36520.1546-0.01170.41870.01640.416620.0201134.261267.886
50.6363-0.25060.10561.78320.02211.2946-0.00070.03440.0205-0.03720.0346-0.0432-0.03570.0353-0.03830.25430.0952-0.01150.34270.02970.344134.0508115.547249.1482
61.53740.2893-0.16551.72450.01350.9835-0.023-0.0060.0595-0.1344-0.06150.0374-0.12620.14770.08510.49920.024-0.06030.26790.00930.384432.5368165.685646.7351
71.30920.19920.05262.30890.12991.6223-0.10720.2516-0.0543-0.76450.0062-0.2182-0.11250.23740.09350.73960.02410.10820.4521-0.00140.432241.688146.781225.3118
81.00170.2444-0.22372.0301-0.00371.2484-0.29920.07130.4074-0.70170.2113-0.1295-0.76340.32140.05951.3833-0.3151-0.07310.79340.14850.867657.3157193.576833.8431
90.34490.47070.05641.0141-0.24650.744-0.59030.7455-0.0011-1.2960.4303-0.6587-0.67690.62360.10351.9764-0.5880.39221.38330.09450.994962.0241177.538.9447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 225)
2X-RAY DIFFRACTION2chain 'B' and (resid -3 through 225)
3X-RAY DIFFRACTION3chain 'C' and (resid -3 through 225)
4X-RAY DIFFRACTION4chain 'D' and (resid -3 through 225)
5X-RAY DIFFRACTION5chain 'E' and (resid -3 through 225)
6X-RAY DIFFRACTION6chain 'F' and (resid -4 through 225)
7X-RAY DIFFRACTION7chain 'G' and (resid -3 through 225)
8X-RAY DIFFRACTION8chain 'H' and (resid -1 through 225)
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 225)

+
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