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- PDB-1f89: Crystal structure of Saccharomyces cerevisiae Nit3, a member of b... -

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Basic information

Entry
Database: PDB / ID: 1f89
TitleCrystal structure of Saccharomyces cerevisiae Nit3, a member of branch 10 of the nitrilase superfamily
Components32.5 KDA PROTEIN YLR351C
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Nitrilase / Dimer / Four layer sandwich / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


omega-amidase / omega-amidase activity / asparagine metabolic process / amide catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / oxaloacetate metabolic process / glutamine metabolic process / Neutrophil degranulation / mitochondrion / cytoplasm
Similarity search - Function
Uncharacterised protein family UPF0012, conserved site / Nit1/2, carbon-nitrogen hydrolase domain / Uncharacterized protein family UPF0012 signature. / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKumaran, D. / Eswaramoorthy, S. / Studier, F.W. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
Citation
Journal: Proteins / Year: 2003
Title: Crystal structure of a putative CN hydrolase from yeast
Authors: Kumaran, D. / Eswaramoorthy, S. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Swaminathan, S.
#1: Journal: CURR.OPIN.STRUCT.BIOL. / Year: 2002
Title: Catalysis in the nitrilase superfamily.
Authors: Brenner, C.
History
DepositionJun 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 32.5 KDA PROTEIN YLR351C
B: 32.5 KDA PROTEIN YLR351C


Theoretical massNumber of molelcules
Total (without water)65,1822
Polymers65,1822
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-13 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.523, 53.492, 80.985
Angle α, β, γ (deg.)90.00, 112.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.70729, 0.019, 0.70667), (0.01867, -0.99979, 0.00819), (0.70668, 0.0074, -0.7075)
Vector: 14.6324, -24.47176, -37.71143)
DetailsThe biological assembly is a dimer.

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Components

#1: Protein 32.5 KDA PROTEIN YLR351C / YLR351C / L9638.5


Mass: 32591.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P49954
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.26 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, HEPES, Magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlprotein1drop
210 %PEG80001reservoir
3100 mMHEPES1reservoir
45 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 14, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 24505 / Num. obs: 24505 / % possible obs: 81.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.429 / Num. unique all: 1062 / % possible all: 35.7
Reflection
*PLUS

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 811 -Random
Rwork0.229 ---
all-23054 --
obs-16521 71.7 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4274 0 0 117 4391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0087
X-RAY DIFFRACTIONc_angle_deg1.536
Refine LS restraints NCSNCS model details: STRICT NON-CRYSTALLOGRAPHIC TWO FOLD
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 2 / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS

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