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- PDB-6dkc: Yeast Ddi2 Cyanamide Hydratase, T157V mutant, apo structure -

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Basic information

Entry
Database: PDB / ID: 6dkc
TitleYeast Ddi2 Cyanamide Hydratase, T157V mutant, apo structure
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 / DNA damage-inducible protein
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 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)238,36050
Polymers234,6979
Non-polymers3,66341
Water4,396244
1
A: DNA damage-inducible protein
hetero molecules

A: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,86210
Polymers52,1552
Non-polymers7078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area4120 Å2
ΔGint-185 kcal/mol
Surface area17790 Å2
MethodPISA
2
B: DNA damage-inducible protein
C: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,34215
Polymers52,1552
Non-polymers1,18813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-262 kcal/mol
Surface area17690 Å2
MethodPISA
3
D: DNA damage-inducible protein
E: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,53517
Polymers52,1552
Non-polymers1,38015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-261 kcal/mol
Surface area18120 Å2
MethodPISA
4
F: DNA damage-inducible protein
G: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7669
Polymers52,1552
Non-polymers6117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-169 kcal/mol
Surface area17980 Å2
MethodPISA
5
H: DNA damage-inducible protein
I: DNA damage-inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2864
Polymers52,1552
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-92 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)263.613, 263.613, 119.026
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7A1Y4, cyanamide hydratase
#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 5.11 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 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: 102026 / % possible obs: 97 % / Redundancy: 5.3 % / Biso Wilson estimate: 53.5 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.6
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.695 / Num. unique obs: 5127 / % possible all: 98.8

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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: 2.9→39.3 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.07
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
Rfree0.2154 2575 2.53 %
Rwork0.1926 --
obs0.1932 101864 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16148 0 169 244 16561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616653
X-RAY DIFFRACTIONf_angle_d0.85822764
X-RAY DIFFRACTIONf_dihedral_angle_d11.6789807
X-RAY DIFFRACTIONf_chiral_restr0.0492619
X-RAY DIFFRACTIONf_plane_restr0.0062916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.95580.25751380.23095554X-RAY DIFFRACTION99
2.9558-3.01610.26231230.22855585X-RAY DIFFRACTION98
3.0161-3.08160.24591540.2245551X-RAY DIFFRACTION98
3.0816-3.15330.25641580.23285478X-RAY DIFFRACTION98
3.1533-3.23210.28111400.22035552X-RAY DIFFRACTION98
3.2321-3.31950.27461270.22725566X-RAY DIFFRACTION98
3.3195-3.41710.26081500.21775516X-RAY DIFFRACTION98
3.4171-3.52730.27111700.2145505X-RAY DIFFRACTION98
3.5273-3.65330.20751710.19725484X-RAY DIFFRACTION98
3.6533-3.79940.21441250.19035517X-RAY DIFFRACTION97
3.7994-3.97220.17121250.17395529X-RAY DIFFRACTION97
3.9722-4.18140.18431420.16785510X-RAY DIFFRACTION97
4.1814-4.44310.16781360.15365469X-RAY DIFFRACTION96
4.4431-4.78560.14761590.15025473X-RAY DIFFRACTION96
4.7856-5.26610.19151200.16575532X-RAY DIFFRACTION96
5.2661-6.02580.21761620.19495458X-RAY DIFFRACTION96
6.0258-7.5830.22391230.21065507X-RAY DIFFRACTION95
7.583-39.32090.23391520.20085503X-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)
10.6373-0.2940.3720.7403-0.4292.3308-0.0907-0.13660.04390.00130.00120.0463-0.2197-0.50630.08180.39710.2251-0.02610.7497-0.00570.389734.855485.208127.3827
20.7736-0.0903-0.24781.5546-0.05731.3712-0.0378-0.111-0.01290.18390.05680.1205-0.2854-0.3842-0.00460.34850.2247-0.01790.60470.03070.381320.7474104.812195.6159
30.84570.0286-0.11261.2864-0.42242.155-0.0031-0.0496-0.0508-0.0444-0.00110.00330.08190.01880.00420.24490.1139-0.03690.38930.0190.328739.12588.449678.4018
40.62820.0165-0.22941.50090.14631.64180.0091-0.10740.05850.13060.0340.0516-0.1293-0.1398-0.03260.30720.153-0.02080.38790.02580.410819.8238133.706467.8311
50.7786-0.2643-0.0731.5369-0.14981.61620.0245-0.0136-0.0019-0.0566-0.0206-0.0513-0.00140.0901-0.0130.2350.0979-0.02260.32270.02350.327933.7927114.858249.0252
61.21380.2611-0.2181.80380.22420.7277-0.0216-0.01880.033-0.1177-0.0546-0.028-0.08190.12880.05720.5130.0364-0.05880.28680.01010.403832.4785165.047646.6497
71.06270.08890.11331.91790.44591.3651-0.09890.1402-0.0895-0.72850.0336-0.1758-0.12340.16730.05840.71550.03080.09110.4270.00080.403841.4967146.084225.128
80.77920.0136-0.43740.8977-0.34460.8372-0.23490.20870.5423-0.77910.2216-0.0372-0.49330.24440.01451.405-0.2827-0.0590.71140.17571.001957.2897192.798833.7994
90.18580.1770.20460.15450.10580.5674-0.62820.80790.0658-1.25050.423-0.5405-0.38030.63130.22421.9305-0.59530.3411.48130.1691.054261.8684176.85898.823
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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