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- PDB-1dwk: STRUCTURE OF CYANASE WITH THE DI-ANION OXALATE BOUND AT THE ENZYM... -

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Basic information

Entry
Database: PDB / ID: 1dwk
TitleSTRUCTURE OF CYANASE WITH THE DI-ANION OXALATE BOUND AT THE ENZYME ACTIVE SITE
ComponentsCYANATE HYDRATASE
KeywordsLYASE / CYANATE DEGRADATION / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


cyanate catabolic process / cyanase / cyanate hydratase activity / DNA binding
Similarity search - Function
Cyanate Lyase; Chain: A, domain 2 / Cyanate lyase, C-terminal domain / : / Cyanate hydratase, N-terminal / Cyanate lyase, C-terminal / Cyanate hydratase / Cyanate lyase, C-terminal domain superfamily / Cyanate lyase C-terminal domain / Cyanate lyase C-terminal domain, Cyanate hydratase / lambda repressor-like DNA-binding domains ...Cyanate Lyase; Chain: A, domain 2 / Cyanate lyase, C-terminal domain / : / Cyanate hydratase, N-terminal / Cyanate lyase, C-terminal / Cyanate hydratase / Cyanate lyase, C-terminal domain superfamily / Cyanate lyase C-terminal domain / Cyanate lyase C-terminal domain, Cyanate hydratase / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
OXALATE ION / Cyanate hydratase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWalsh, M.A. / Otwinowski, Z. / Perrakis, A. / Anderson, P.M. / Joachimiak, A.
Citation
Journal: Structure / Year: 2000
Title: Structure of Cyanase Reveals that a Novel Dimeric and Decameric Arrangement of Subunits is Required for Formation of the Enzyme Active Site.
Authors: Walsh, M.A. / Otwinowski, Z. / Perrakis, A. / Anderson, P.M. / Joachimiak, A.
#1: Journal: J.Bacteriol. / Year: 1987
Title: Characterization of High-Level Expression and Sequencing of the Escherichia Coli K-12 Cyns Gene Encoding Cyanase.
Authors: Sung, Y. / Anderson, P.M. / Fuchs, J.A.
#2: Journal: Biochemistry / Year: 1986
Title: Kinetic Properties of Cyanase.
Authors: Anderson, P.M. / Little, R.M.
#3: Journal: Biochemistry / Year: 1986
Title: Interaction of Mono- and Dianions with Cyanase: Evidence for Apparent Half-Site Binding.
Authors: Anderson, P.M. / Johnson, W.V. / Endrizzi, J.A. / Little, R.M. / Korte, J.J.
#4: Journal: Biochemistry / Year: 1980
Title: Purification and Properties of the Inducible Enzyme Cyanase.
Authors: Anderson, P.M.
History
DepositionDec 7, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations / Category: database_PDB_caveat / struct_conn / Item: _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEET STRUCTURE OF THIS ASSEMBLY IS COMPRISED OF FIVE SHEETS ... SHEET DETERMINATION METHOD: DSSP THE SHEET STRUCTURE OF THIS ASSEMBLY IS COMPRISED OF FIVE SHEETS THAT FORM AN EQUATORIAL GIRDLE AROUND THE DECAMERIC ASSEMBLY. EACH SHEET IS MADE UP OF FOUR STRANDS FROM TWO PROTEIN CHAINS EACH CONTRIBUTING TWO STRANDS

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYANATE HYDRATASE
B: CYANATE HYDRATASE
C: CYANATE HYDRATASE
D: CYANATE HYDRATASE
E: CYANATE HYDRATASE
F: CYANATE HYDRATASE
G: CYANATE HYDRATASE
H: CYANATE HYDRATASE
I: CYANATE HYDRATASE
J: CYANATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,20338
Polymers172,55410
Non-polymers2,65028
Water44,3892464
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area71470 Å2
ΔGint-728 kcal/mol
Surface area46590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.330, 80.930, 82.130
Angle α, β, γ (deg.)70.10, 71.95, 66.42
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.93999, -0.17058, -0.29551), (-0.21224, 0.3858, -0.89784), (0.26716, 0.90668, 0.32644)4.45768, 12.76704, 16.74146
2given(-0.95538, 0.17904, -0.23492), (0.15902, -0.35845, -0.9199), (-0.2489, -0.91622, 0.31399)-32.94405, 21.10961, 8.98303
3given(-0.84248, 0.50836, 0.17832), (0.51211, 0.65297, 0.558), (0.16723, 0.56143, -0.81045)-38.72794, -0.11411, 35.81633
4given(0.84717, -0.49463, -0.19401), (-0.50957, -0.65297, -0.56033), (0.15047, 0.57356, -0.80522)1.3132, 2.1657, 35.65663
5given(-0.93217, 0.20223, 0.30026), (0.21386, -0.3616, 0.90747), (0.2921, 0.91014, 0.29383)-42.29507, -11.38524, 17.79961
6given(-0.99949, 0.00441, 0.03164), (-0.00436, -0.99999, 0.00153), (0.03165, 0.00139, 0.9995)-38.4437, 1.81054, 0.82802
7given(0.85187, -0.50724, 0.13048), (-0.48349, -0.66581, 0.56827), (-0.20137, -0.54718, -0.81243)-4.5825, -18.01904, 30.11536
8given(0.94433, -0.21791, 0.24647), (-0.15897, 0.35364, 0.92177), (-0.28803, -0.90964, 0.29931)-5.10585, -19.28598, 8.44793
9given(-0.85947, 0.48484, -0.16197), (0.48111, 0.66015, -0.57683), (-0.17275, -0.57369, -0.80065)-32.666, 20.07861, 30.47783
DetailsHOMODECAMER OF CYANASE CONTAINS 5 CATALYTIC SITES.IN EACH OF THESE SITES AN OXALATE ION WHICH IS ACOMPETITIVE INHIBITOR OF CYANASE IS BOUND.

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Components

#1: Protein
CYANATE HYDRATASE


Mass: 17255.377 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00816, cyanase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2464 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.3
Details: SELENOMETHIONINE LABELLED CRYSTALS WERE GROWN BY THE SITTING DROP METHOD OF VAPOUR DIFFUSION FROM 50% AMMONIUM SULPHATE SOLUTIONS BUFFERED WITH 50MM NAKPO4, PH = 7.3, AND IN THE PRESENCE OF ...Details: SELENOMETHIONINE LABELLED CRYSTALS WERE GROWN BY THE SITTING DROP METHOD OF VAPOUR DIFFUSION FROM 50% AMMONIUM SULPHATE SOLUTIONS BUFFERED WITH 50MM NAKPO4, PH = 7.3, AND IN THE PRESENCE OF 50 MM TRIC/HCL, PH =7.3. MICROSEEDING WITH WILD-TYPE CRYSTALS PRODUCED CRYSTALS THAT GREW TO 0.1 X 0.2 X 0.7 MM**3 OVER 5-7 DAYS. CRYSTALS WERE THEN SOAKED FOR 4 HOURS IN 5 MM SODIUM OXALATE BEFORE BEING FLASH FROZEN.
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.1 Mammp,ium sulfate1reservoir
250 mM1reservoirNaKPO4
350 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0335
DetectorType: ARGONNE APS-1 / Detector: CCD / Date: Nov 15, 1998 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0335 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 190231 / % possible obs: 95.4 % / Redundancy: 2.3 % / Biso Wilson estimate: 13.4 Å2 / Rsym value: 0.047 / Net I/σ(I): 26.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.171 / % possible all: 79.4
Reflection
*PLUS
Num. measured all: 436555 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 79.4 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DW9

1dw9


Resolution: 1.65→20 Å / SU B: 1.07 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.088
Details: NCS RESTRAINTS NOT EMPLOYED ALTERNATIVE CONFORMATIONS WERE MODELLED FOR THE FOLLOWING AMINO ACID SIDE CHAINS CHAIN A: 25 27 31 34 60 66 78 101 132 133 CHAIN B: 10 27 66 78 101 128 CHAIN C: ...Details: NCS RESTRAINTS NOT EMPLOYED ALTERNATIVE CONFORMATIONS WERE MODELLED FOR THE FOLLOWING AMINO ACID SIDE CHAINS CHAIN A: 25 27 31 34 60 66 78 101 132 133 CHAIN B: 10 27 66 78 101 128 CHAIN C: 27 40 60 78 88 101 128 132 CHAIN D: 27 78 101 128 133 CHAIN E: 27 31 34 78 101 128 CHAIN F: 60 78 101 128 CHAIN G: 25 27 34 40 78 101 128 CHAIN H: 31 78 101 128 CHAIN I: 101 128 CHAIN J: 27 31 40 78 101 128 THIS STRUCTURE WAS DETERMINED AS PART OF THE STRUCTURAL GENOMICS INITIATIVE AT ARGONNE NATIONAL LABORATORY
RfactorNum. reflection% reflectionSelection details
Rfree0.181 9561 3 %RANDOM
Rwork0.146 ---
obs0.138 190161 95.4 %-
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11970 0 145 2464 14579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.382
X-RAY DIFFRACTIONp_mcangle_it1.793
X-RAY DIFFRACTIONp_scbond_it2.412
X-RAY DIFFRACTIONp_scangle_it3.223
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1550.15
X-RAY DIFFRACTIONp_singtor_nbd0.1860.3
X-RAY DIFFRACTIONp_multtor_nbd0.2580.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.67
X-RAY DIFFRACTIONp_staggered_tor12.720
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.139 / Rfactor Rfree: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.031

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