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- PDB-2ivg: SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYT... -

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Basic information

Entry
Database: PDB / ID: 2ivg
TitleSITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE
ComponentsCYANATE LYASE
KeywordsLYASE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / MCSG / CYANATE DEGRADATION
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
AZIDE ION / Cyanate hydratase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsGuilloton, M. / Walsh, M.A. / Joachimiak, A. / Anderson, P.M.
Citation
Journal: To be Published
Title: A Twin Set of Low Pka Arginines Ensures the Concerted Acid Base Catalytic Mechanism of Cyanase
Authors: Guilloton, M. / Walsh, M.A. / Joachimiak, A. / Anderson, P.M.
#1: 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.
History
DepositionJun 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_validate_close_contact / struct_conn
Item: _atom_site.label_alt_id / _pdbx_validate_close_contact.label_alt_id_2
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 2.2Dec 13, 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

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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)173,65460
Polymers170,11710
Non-polymers3,53750
Water31,5981754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72770 Å2
ΔGint-541.6 kcal/mol
Surface area61160 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.392, 80.897, 81.094
Angle α, β, γ (deg.)70.69, 75.98, 65.15
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.94288, -0.19293, 0.27158), (-0.18638, 0.37021, 0.91006), (-0.27612, -0.90869, 0.31311)0.0291, 0.11926, 0.13584
2given(-0.94413, 0.18546, -0.27243), (0.18819, -0.3752, -0.90764), (-0.27055, -0.9082, 0.31934)-0.08489, -0.08726, 0.12545
3given(-0.93578, 0.20555, 0.28646), (0.19858, -0.36409, 0.90995), (0.29134, 0.9084, 0.29989)0.08568, 0.09847, -0.02345
4given(0.84322, -0.51122, 0.16625), (-0.50675, -0.65268, 0.56322), (-0.17942, -0.55916, -0.80941)0.03273, 0.01788, -0.03464
5given(-0.84303, 0.50829, 0.17588), (0.5115, 0.6565, 0.55441), (0.16634, 0.55735, -0.81344)0.04835, 0.06728, -0.0264
6given(-0.84641, 0.50371, -0.17284), (0.50299, 0.64956, -0.57015), (-0.17492, -0.56952, -0.80315)-0.02697, -0.12412, 0.02926
7given(0.84425, -0.50454, -0.18077), (-0.51061, -0.65472, -0.55733), (0.16284, 0.56283, -0.81037)-0.04989, -0.04217, -0.0485
8given(0.93952, -0.19386, -0.28234), (-0.19825, 0.3644, -0.9099), (0.27928, 0.91084, 0.30392)-0.0613, -0.15796, -0.11347
9given(-0.99997, 0.00037, 0.00789), (-0.00032, -0.99998, 0.00669), (0.0079, 0.00668, 0.99995)-0.04909, 0.00373, 0.02695

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Components

#1: Protein
CYANATE LYASE / CYANASE LYASE / CYANASE / CYANATE HYDROLASE


Mass: 17011.686 Da / Num. of mol.: 10 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P00816, cyanase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1754 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN B, LEU 151 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN B, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN C, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN D, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN E, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN F, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN G, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN H, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN I, LEU 151 TO GLY ENGINEERED RESIDUE IN CHAIN J, LEU 151 TO GLY
Sequence detailsLEUCINE 151 MUTATED TO GLYCINE

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.3
Details: CRYSTALLIZATION CONDITIONS: 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 ...Details: CRYSTALLIZATION CONDITIONS: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.87→99 Å / Num. obs: 133334 / % possible obs: 95.1 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.6
Reflection shellResolution: 1.87→1.93 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DW9

1dw9


Resolution: 1.87→76.7 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.368 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 6673 5 %RANDOM
Rwork0.145 ---
obs0.147 126659 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0 Å2-0.01 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.87→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11940 0 168 1754 13862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02212305
X-RAY DIFFRACTIONr_bond_other_d0.0020.028310
X-RAY DIFFRACTIONr_angle_refined_deg1.6382.01816674
X-RAY DIFFRACTIONr_angle_other_deg1.159320471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15251576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03424.898490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.195152235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1121570
X-RAY DIFFRACTIONr_chiral_restr0.1070.21956
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022253
X-RAY DIFFRACTIONr_nbd_refined0.2170.22536
X-RAY DIFFRACTIONr_nbd_other0.2150.28885
X-RAY DIFFRACTIONr_nbtor_refined0.1720.25931
X-RAY DIFFRACTIONr_nbtor_other0.080.26584
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21378
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2990.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.31.510083
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38212504
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.86535049
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7354.54157
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.92 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.245 454
Rwork0.172 8903

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