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

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Basic information

Entry
Database: PDB / ID: 2ivq
TitleSITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE
ComponentsCYANATE HYDRATASE
KeywordsLYASE / CYANATE DEGRADATION / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 14, 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 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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 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)173,16447
Polymers170,39810
Non-polymers2,76637
Water20,2491124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74850 Å2
ΔGint-526.9 kcal/mol
Surface area61920 Å2
MethodPQS
Unit cell
Length a, b, c (Å)76.883, 80.845, 82.647
Angle α, β, γ (deg.)69.99, 71.98, 66.17
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.94203, -0.17328, -0.28732), (-0.20766, 0.37149, -0.90492), (0.26354, 0.91212, 0.31397)0.04276, -0.10161, 0.03755
2given(-0.95486, 0.17402, -0.24075), (0.16428, -0.36587, -0.91605), (-0.24749, -0.91425, 0.32076)-0.02533, -0.04205, 0.02238
3given(-0.84602, 0.50492, 0.17122), (0.50666, 0.6614, 0.55304), (0.16599, 0.55463, -0.81537)-0.10362, 0.13723, -0.09119
4given(0.85028, -0.4914, -0.18856), (-0.50468, -0.65947, -0.55713), (0.14942, 0.56888, -0.80874)0.19696, -0.02381, 0.05375
5given(-0.93463, 0.2005, 0.2937), (0.20877, -0.35921, 0.90961), (0.28788, 0.91146, 0.29387)0.00077, 0.03906, 0.04655
6given(-0.99954, 0.00568, 0.02971), (-0.00552, -0.99997, 0.00542), (0.02974, 0.00526, 0.99954)-0.01072, 0.07946, 0.10252
7given(0.85249, -0.50525, 0.13407), (-0.48377, -0.66539, 0.56852), (-0.19804, -0.54952, -0.81167)0.17549, 0.01329, -0.10419
8given(0.94496, -0.20458, 0.25534), (-0.17035, 0.35868, 0.91779), (-0.27935, -0.91077, 0.30409)0.0383, 0.06496, 0.00746
9given(0.94496, -0.20458, 0.25534), (-0.17035, 0.35868, 0.91779), (-0.27935, -0.91077, 0.30409)0.0383, 0.06496, 0.00746

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Components

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


Mass: 17039.779 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.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE REACTION OF CYANATE WITH BICARBONATE TO PRODUCE AMMONIA AND CARBON DIOXIDE. ...CATALYZES THE REACTION OF CYANATE WITH BICARBONATE TO PRODUCE AMMONIA AND CARBON DIOXIDE. ENGINEERED RESIDUE IN CHAIN A, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN B, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN C, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN D, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN E, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN F, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN G, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN H, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN I, ARG 96 TO LYS ENGINEERED RESIDUE IN CHAIN J, ARG 96 TO LYS
Sequence detailsARGININE 96 MUTATED TO LYSINE

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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 % / Description: NONE
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 OF ...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: 2.1→50 Å / Num. obs: 93895 / % possible obs: 98 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 11.9 / % possible all: 96.7

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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: 2.1→76.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.897 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4687 5 %RANDOM
Rwork0.18 ---
obs0.183 89022 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å21.96 Å2-2.43 Å2
2---1.36 Å2-0.43 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→76.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11960 0 133 1124 13217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02212240
X-RAY DIFFRACTIONr_bond_other_d0.0010.028268
X-RAY DIFFRACTIONr_angle_refined_deg1.8352.01816564
X-RAY DIFFRACTIONr_angle_other_deg1.069320398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09751554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13925.208480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.789152248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7141560
X-RAY DIFFRACTIONr_chiral_restr0.1090.21952
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022202
X-RAY DIFFRACTIONr_nbd_refined0.2210.22773
X-RAY DIFFRACTIONr_nbd_other0.2050.28884
X-RAY DIFFRACTIONr_nbtor_refined0.1740.25798
X-RAY DIFFRACTIONr_nbtor_other0.0870.26472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.21044
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1661.59981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.405212462
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.54135008
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4114.54100
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 303
Rwork0.245 5512

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