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- PDB-4hg3: Structural insights into yeast Nit2: wild-type yeast Nit2 in comp... -

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Basic information

Entry
Database: PDB / ID: 4hg3
TitleStructural insights into yeast Nit2: wild-type yeast Nit2 in complex with alpha-ketoglutarate
ComponentsProbable hydrolase NIT2
KeywordsHYDROLASE / nitrilase superfamily / omega-amidase
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
2-OXOGLUTARIC ACID / CACODYLATE ION / Deaminated glutathione amidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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
DepositionOct 6, 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 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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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)156,19231
Polymers153,1754
Non-polymers3,01727
Water11,097616
1
A: Probable hydrolase NIT2
C: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,25717
Polymers76,5882
Non-polymers1,66915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-13 kcal/mol
Surface area24660 Å2
MethodPISA
2
B: Probable hydrolase NIT2
D: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,93514
Polymers76,5882
Non-polymers1,34812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-13 kcal/mol
Surface area23900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.211, 125.653, 77.964
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable hydrolase NIT2


Mass: 38293.809 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: NIT2, YJL126W, J0706 / Production host: Escherichia coli (E. coli)
References: UniProt: P47016, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17.5% PEG4000, 0.1M sodium cacodylate, 25mM 2-oxoglutaric acid sodium salt, 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: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 92926 / Num. obs: 92897 / % possible obs: 100 % / Observed criterion σ(I): 2.6
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H5U

4h5u


Resolution: 1.93→48.84 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.54 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22675 4631 5 %RANDOM
Rwork0.19682 ---
obs0.19833 87911 99.35 %-
all-92775 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20.05 Å2
2--0.21 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9455 0 167 616 10238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229836
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.98813292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75351201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25924.339431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.309151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6791568
X-RAY DIFFRACTIONr_chiral_restr0.0670.21481
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217270
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.371.56015
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70229734
X-RAY DIFFRACTIONr_scbond_it1.00833821
X-RAY DIFFRACTIONr_scangle_it1.7054.53553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.984 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 325 -
Rwork0.238 6292 -
obs--96.39 %

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