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- PDB-6dka: Yeast Ddi2 Cyanamide Hydratase -

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Basic information

Entry
Database: PDB / ID: 6dka
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 / CYANAMIDE / DNA damage-inducible protein
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.901 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)238,07851
Polymers234,6979
Non-polymers3,38142
Water4,774265
1
A: DNA damage-inducible protein
hetero molecules

A: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,94612
Polymers52,1552
Non-polymers79110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area4510 Å2
ΔGint-186 kcal/mol
Surface area17830 Å2
MethodPISA
2
B: DNA damage-inducible protein
C: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,23415
Polymers52,1552
Non-polymers1,07913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-230 kcal/mol
Surface area17750 Å2
MethodPISA
3
D: DNA damage-inducible protein
E: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,13814
Polymers52,1552
Non-polymers98312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-214 kcal/mol
Surface area18100 Å2
MethodPISA
4
F: DNA damage-inducible protein
G: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,85011
Polymers52,1552
Non-polymers6959
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-157 kcal/mol
Surface area18070 Å2
MethodPISA
5
H: DNA damage-inducible protein
I: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3825
Polymers52,1552
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-101 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)263.430, 263.430, 119.214
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: 26077.482 Da / Num. of mol.: 9 / Mutation: T157V
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-CNN / CYANAMIDE / Cyanamide


Mass: 42.040 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 5.09 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 Sulfate 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: 2.9→39.3 Å / Num. obs: 101420 / % possible obs: 96.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 55.6 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 16.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5107 / % possible all: 98.4

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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: 2.901→29.966 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.19
Details: Iterative maximum lilelihood 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 lilelihood 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
Rfree0.2296 2569 2.53 %
Rwork0.1978 --
obs0.1986 101380 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.901→29.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16158 0 160 265 16583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616677
X-RAY DIFFRACTIONf_angle_d0.84522788
X-RAY DIFFRACTIONf_dihedral_angle_d11.4869838
X-RAY DIFFRACTIONf_chiral_restr0.052625
X-RAY DIFFRACTIONf_plane_restr0.0062925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9011-2.95680.30281400.27235432X-RAY DIFFRACTION97
2.9568-3.01710.26351380.25795552X-RAY DIFFRACTION98
3.0171-3.08270.30161540.25145529X-RAY DIFFRACTION98
3.0827-3.15430.29021360.24735482X-RAY DIFFRACTION98
3.1543-3.23310.26731290.23355559X-RAY DIFFRACTION98
3.2331-3.32040.26461590.23375497X-RAY DIFFRACTION98
3.3204-3.4180.24911440.22335507X-RAY DIFFRACTION97
3.418-3.52820.21871280.20995489X-RAY DIFFRACTION97
3.5282-3.6540.18451130.19075509X-RAY DIFFRACTION97
3.654-3.80010.20871120.18655482X-RAY DIFFRACTION97
3.8001-3.97270.21991490.1835464X-RAY DIFFRACTION96
3.9727-4.18160.22411460.16985467X-RAY DIFFRACTION96
4.1816-4.44280.18571480.15725468X-RAY DIFFRACTION96
4.4428-4.78450.191520.15595456X-RAY DIFFRACTION96
4.7845-5.26370.22881640.1695466X-RAY DIFFRACTION96
5.2637-6.020.20221640.19885482X-RAY DIFFRACTION96
6.02-7.56430.22911560.21135471X-RAY DIFFRACTION95
7.5643-29.96790.26051370.20175499X-RAY DIFFRACTION93
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)
10.9309-0.0880.34441.3988-0.20982.768-0.0646-0.12080.08620.00860.03780.0952-0.1725-0.50920.04230.3450.2367-0.01510.70610.01220.352234.792885.1313127.5125
21.1117-0.2176-0.09981.9883-0.14511.7103-0.0332-0.11130.04010.20850.09380.1724-0.304-0.3737-0.04840.35790.24420.00540.64290.06160.41220.7334104.679895.6517
31.3834-0.3076-0.08961.5627-0.36312.6524-0.0156-0.0062-0.0378-0.03080.00180.04340.10840.05990.00620.23760.1377-0.02630.4530.01490.333939.060388.28878.476
40.8551-0.0688-0.05021.78040.13981.7782-0.0361-0.08130.0450.12990.06230.0656-0.2097-0.1647-0.00380.36020.193-0.00820.4190.04850.42419.767133.539167.8588
51.148-0.44350.10571.60940.01972.01540.0114-0.0626-0.0093-0.041-0.0179-0.0214-0.06140.0561-0.00620.26250.1255-0.01270.38470.0530.348133.7106114.683148.969
61.50760.1806-0.36372.1010.20181.7498-0.0855-0.03860.1181-0.1269-0.04070.013-0.22380.15760.13230.58990.0158-0.10810.28690.01990.460132.539164.832846.7364
71.5031-0.1140.32753.1230.29861.9087-0.13220.2473-0.0017-0.840.0432-0.188-0.14980.26870.09410.73040.01080.06960.41730.0420.374241.4088145.934625.0721
81.85870.6057-0.51721.3354-0.15311.4814-0.22450.16170.8532-0.76260.1280.1334-0.63770.36150.07061.2237-0.2765-0.15070.66180.2171.084657.252192.579833.8741
90.2103-0.0170.38190.98680.88420.9845-0.62690.78230.4007-1.41410.5153-0.5018-0.35620.51620.06331.7378-0.53530.30571.40940.2881.060661.5988176.88638.8054
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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