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Basic information

Entry
Database: PDB / ID: 1dw9
TitleStructure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site
ComponentsCYANATE LYASE
KeywordsLYASE / CYANATE DEGRADATION / STRUCTURAL GENOMICS / 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
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsWalsh, M.A. / Otwinowski, Z. / Perrakis, A. / Anderson, P.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
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 3, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.2Sep 28, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 LYASE
B: CYANATE LYASE
C: CYANATE LYASE
D: CYANATE LYASE
E: CYANATE LYASE
F: CYANATE LYASE
G: CYANATE LYASE
H: CYANATE LYASE
I: CYANATE LYASE
J: CYANATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,11843
Polymers172,55410
Non-polymers2,56433
Water33,5981865
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area73320 Å2
ΔGint-480.9 kcal/mol
Surface area62230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.340, 81.030, 82.300
Angle α, β, γ (deg.)70.30, 72.20, 66.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.94065, -0.17222, -0.29243), (-0.20872, 0.38587, -0.89863), (0.2676, 0.90634, 0.32702)4.36759, 12.8399, 16.75605
2given(-0.95355, 0.18279, -0.23944), (0.16297, -0.35548, -0.92037), (-0.25335, -0.91664, 0.30918)-32.81829, 21.16895, 8.98718
3given(-0.84309, 0.50703, 0.17922), (0.51082, 0.65086, 0.56165), (0.16813, 0.56507, -0.80773)-38.81259, -0.18068, 35.79026
4given(0.84717, -0.49605, -0.19036), (-0.50816, -0.65182, -0.56295), (0.15518, 0.57364, -0.80427)1.2514, 2.20191, 35.70566
5given(-0.93414, 0.19954, 0.29591), (0.20986, -0.36354, 0.90763), (0.28869, 0.90995, 0.29773)-42.29295, -11.4549, 17.69791
6given(-0.99967, 0.00341, 0.02539), (-0.00344, -0.99999, -0.00084), (0.02539, -0.00093, 0.99968)-38.32463, 1.86082, 0.72657
7given(0.85152, -0.50635, 0.13612), (-0.48606, -0.66493, 0.56711), (-0.19664, -0.54907, -0.81232)-4.6391, -18.07603, 30.19
8given(0.94416, -0.21624, 0.24859), (-0.16169, 0.35332, 0.92143), (-0.28709, -0.91017, 0.29862)-5.10082, -19.33665, 8.45441
9given(-0.8582, 0.48703, -0.16216), (0.48354, 0.66099, -0.57384), (-0.17229, -0.57088, -0.80275)-32.6452, 20.0779, 30.519

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Components

#1: Protein
CYANATE LYASE / CYANATE HYDROLASE / CYANASE


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, EC: 4.3.99.1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1865 / 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 OVER 5-7 DAYS.
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, sitting drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.1 Mammonium sulfate1drop
250 mM1dropNaKPO4
350 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9465, 0.9793, 0.9795, 1.033, 1.078, 1.00
DetectorType: ARGONNE APS-1 / Detector: CCD / Date: Jul 15, 1998 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94651
20.97931
30.97951
41.0331
51.0781
611
ReflectionResolution: 1.65→20 Å / Num. obs: 187107 / % possible obs: 94.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.039 / Net I/σ(I): 26.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.198 / % possible all: 80.6
Reflection
*PLUS
Num. measured all: 524489 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 80.6 % / Rmerge(I) obs: 0.198

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→20 Å / SU B: 1.66 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.092
Details: NCS RESTRAINTS NOT EMPLOYED ALTERNATIVE CONFORMATIONS WERE MODELLED FOR THE FOLLOWING AMINO ACID SIDE CHAINS CHAIN A: 25 27 31 34 66 78 101 128 132 133 CHAIN B: 10 27 60 66 78 101 128 131 ...Details: NCS RESTRAINTS NOT EMPLOYED ALTERNATIVE CONFORMATIONS WERE MODELLED FOR THE FOLLOWING AMINO ACID SIDE CHAINS CHAIN A: 25 27 31 34 66 78 101 128 132 133 CHAIN B: 10 27 60 66 78 101 128 131 CHAIN C: 27 40 60 78 88 101 128 132 CHAIN D: 27 78 101 128 133 CHAIN E: 27 31 34 40 78 101 128 CHAIN F: 40 60 78 101 128 CHAIN G: 25 27 34 78 101 128 CHAIN H: 31 40 78 101 128 CHAIN I: 27 60 101 128 CHAIN J: 27 31 78 101 128 THIS STRUCTURE WAS DETERMINED AS PART OF THE STRUCTURAL GENOMICS INITIATIVE AT ARGONNE NATIONAL LABORATORY
RfactorNum. reflection% reflectionSelection details
Rfree0.189 9436 3 %RANDOM
Rwork0.15 ---
obs-177665 94.2 %-
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11970 0 125 1865 13960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.622
X-RAY DIFFRACTIONp_mcangle_it2.143
X-RAY DIFFRACTIONp_scbond_it2.742
X-RAY DIFFRACTIONp_scangle_it3.993
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.47
X-RAY DIFFRACTIONp_staggered_tor1320
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: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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