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- PDB-4h5u: Structural insights into yeast Nit2: wild-type yeast Nit2 -

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Basic information

Entry
Database: PDB / ID: 4h5u
TitleStructural insights into yeast Nit2: wild-type yeast Nit2
ComponentsProbable hydrolase NIT2
KeywordsHYDROLASE / similar to mouse Nit2 / probable CN hydolase
Function / homology
Function and homology information


deaminated glutathione amidase / [acetyl-CoA carboxylase]-phosphatase activity / deaminated glutathione amidase activity / amide catabolic process / mitochondrion
Similarity search - Function
Nit1/2, carbon-nitrogen hydrolase domain / Uncharacterised protein family UPF0012, conserved site / Uncharacterized protein family UPF0012 signature. / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Deaminated glutathione amidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLiu, H. / Qiu, X. / Zhang, M. / Gao, Y. / Niu, L. / Teng, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2
Authors: Liu, H. / Gao, Y. / Zhang, M. / Qiu, X. / Cooper, A.J.L. / Niu, L. / Teng, M.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Structure summary
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable hydrolase NIT2
B: Probable hydrolase NIT2
C: Probable hydrolase NIT2
D: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,98918
Polymers153,6554
Non-polymers1,33414
Water14,124784
1
A: Probable hydrolase NIT2
hetero molecules

C: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3808
Polymers76,8282
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3740 Å2
ΔGint-30 kcal/mol
Surface area24030 Å2
MethodPISA
2
B: Probable hydrolase NIT2
hetero molecules

D: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,60910
Polymers76,8282
Non-polymers7828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area3890 Å2
ΔGint-30 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.262, 125.665, 77.674
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable hydrolase NIT2


Mass: 38413.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: J0706, NIT2, YJL126W / Production host: Escherichia coli (E. coli)
References: UniProt: P47016, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17.5% PEG4000, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97792 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 21, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97792 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 95100 / Num. obs: 95100 / % possible obs: 100 % / Observed criterion σ(I): 4.66
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 4.81 / Num. unique all: 4714 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASER2.1.4phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMS

1ems


Resolution: 1.92→48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20228 4767 5 %RANDOM
Rwork0.17078 ---
all0.1724 95100 --
obs0.1724 90290 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0.03 Å2
2--0.52 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.92→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9441 0 83 784 10308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.01310.0229767
X-RAY DIFFRACTIONr_angle_refined_deg1.15971.98213219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80551212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61724.376425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.946151730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1181563
X-RAY DIFFRACTIONr_chiral_restr0.0770.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217224
X-RAY DIFFRACTIONr_mcbond_it0.4771.56033
X-RAY DIFFRACTIONr_mcangle_it0.88629759
X-RAY DIFFRACTIONr_scbond_it1.23733734
X-RAY DIFFRACTIONr_scangle_it2.1354.53449
LS refinement shellResolution: 1.92→1.967 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 320 -
Rwork0.207 6451 -
obs--96.3 %

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