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- PDB-6dkd: Yeast Ddi2 Cyanamide Hydratase -

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Basic information

Entry
Database: PDB / ID: 6dkd
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 / FOURIER SYNTHESIS / Resolution: 3 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 1.3Oct 11, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)237,68145
Polymers234,4999
Non-polymers3,18236
Water3,189177
1
A: DNA damage-inducible protein
hetero molecules

A: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6268
Polymers52,1112
Non-polymers5156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area3640 Å2
ΔGint-148 kcal/mol
Surface area17840 Å2
MethodPISA
2
B: DNA damage-inducible protein
C: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,10613
Polymers52,1112
Non-polymers99511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-225 kcal/mol
Surface area17910 Å2
MethodPISA
3
D: DNA damage-inducible protein
E: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,29815
Polymers52,1112
Non-polymers1,18813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-258 kcal/mol
Surface area18050 Å2
MethodPISA
4
F: DNA damage-inducible protein
G: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7229
Polymers52,1112
Non-polymers6117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-154 kcal/mol
Surface area17770 Å2
MethodPISA
5
H: DNA damage-inducible protein
I: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2424
Polymers52,1112
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-93 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.643, 264.643, 119.304
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
DNA damage-inducible protein


Mass: 26055.410 Da / Num. of mol.: 9 / Mutation: H137N
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.: 27 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.14 Å3/Da / Density % sol: 76 % / Description: flattened discs
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 1.1-1.3 M Ammonium Sulphate 0.2 M Arginine 0.1 M N-morpholino ethane sulfonate pH 5.8
PH range: 5.2-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0246 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 20, 2016 / Details: Toroidal Focusing Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0246 Å / Relative weight: 1
ReflectionResolution: 3→39.8 Å / Num. obs: 92614 / % possible obs: 96.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 66.2 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4667 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6DK9

6dk9


Resolution: 3→39.768 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.97
Details: 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 ...Details: 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
Rfree0.2205 2309 2.49 %
Rwork0.1944 --
obs0.1951 92551 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→39.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16042 0 144 177 16363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616516
X-RAY DIFFRACTIONf_angle_d0.94722585
X-RAY DIFFRACTIONf_dihedral_angle_d12.1039742
X-RAY DIFFRACTIONf_chiral_restr0.0512612
X-RAY DIFFRACTIONf_plane_restr0.0082902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.06520.32461260.27485673X-RAY DIFFRACTION97
3.0652-3.13650.26931430.24735692X-RAY DIFFRACTION98
3.1365-3.21490.28371580.23655646X-RAY DIFFRACTION98
3.2149-3.30180.25821330.23955681X-RAY DIFFRACTION98
3.3018-3.39890.28721390.24275663X-RAY DIFFRACTION97
3.3989-3.50850.25321150.2245697X-RAY DIFFRACTION98
3.5085-3.63380.26111380.20885663X-RAY DIFFRACTION97
3.6338-3.77920.21281550.20075629X-RAY DIFFRACTION97
3.7792-3.95110.18561440.18835657X-RAY DIFFRACTION97
3.9511-4.15920.21591570.17675634X-RAY DIFFRACTION97
4.1592-4.41940.16831250.1595645X-RAY DIFFRACTION96
4.4194-4.76020.1751650.1555616X-RAY DIFFRACTION96
4.7602-5.23820.18781390.17015609X-RAY DIFFRACTION96
5.2382-5.9940.23361580.19395587X-RAY DIFFRACTION95
5.994-7.54340.25581510.20485569X-RAY DIFFRACTION94
7.5434-39.77150.20421630.18065581X-RAY DIFFRACTION92
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)
10.9118-0.00070.03211.0222-0.13851.9025-0.0363-0.06160.10520.0193-0.11830.0874-0.2085-0.50040.08980.52720.316-0.05241.0597-0.0510.444734.962885.4453127.6127
20.7474-0.14660.01541.42440.0141.20420.0098-0.16950.03320.2156-0.03270.1449-0.3272-0.4435-0.0090.49330.3686-0.0330.9430.00570.473220.7354105.127895.6511
31.4032-0.38370.08161.2144-0.22421.9581-0.0906-0.1307-0.053-0.00010.0345-0.05120.11580.0230.03380.34640.1872-0.03150.57410.0280.410139.236388.793578.5141
40.81520.02910.04551.50660.22651.3289-0.0153-0.09390.06680.14920.02470.0523-0.1087-0.04270.0010.40390.186-0.04060.47450.02980.47519.8199134.261767.7665
51.0146-0.8272-0.05721.4898-0.14651.28940.01560.0643-0.0215-0.0286-0.0044-0.1099-0.01180.1386-0.0020.33040.1463-0.04580.47490.02890.422133.89115.257449.0517
61.16820.3864-0.27411.6136-0.05881.0967-0.025-0.01120.0774-0.1508-0.07160.0102-0.18350.16620.05030.61350.0261-0.06720.3436-0.00490.503132.6454165.721346.6537
70.65490.08910.10342.00730.22811.2414-0.02460.1596-0.0868-0.7399-0.105-0.1499-0.07010.17550.0910.85170.08660.10790.5419-0.02860.508641.7644146.675325.2082
80.5127-0.048-0.16010.43140.25090.1687-0.25570.12830.4793-1.02120.2155-0.2443-0.61360.37420.01212.0303-0.4407-0.07790.94350.19821.086557.9536193.226933.8925
90.2190.41310.02921.1259-0.45340.7624-0.49030.75550.1398-1.39210.3684-0.7157-1.2131.01130.15372.7425-0.85270.4241.84650.13161.203963.1243176.7599.1028
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 0 through 225)
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 225)

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