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- PDB-4hgd: Structural insights into yeast Nit2: C169S mutant of yeast Nit2 i... -

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Basic information

Entry
Database: PDB / ID: 4hgd
TitleStructural insights into yeast Nit2: C169S mutant of yeast Nit2 in complex with an endogenous peptide-like ligand
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
CACODYLATE ION / N-(4-carboxy-4-oxobutanoyl)-L-cysteinylglycine / Deaminated glutathione amidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 8, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 20, 2024Group: Source and taxonomy / Category: entity_src_nat

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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)156,08125
Polymers153,1114
Non-polymers2,97021
Water5,945330
1
A: Probable hydrolase NIT2
D: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,17914
Polymers76,5552
Non-polymers1,62312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-30 kcal/mol
Surface area22920 Å2
MethodPISA
2
B: Probable hydrolase NIT2
C: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,90311
Polymers76,5552
Non-polymers1,3479
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-30 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.632, 126.915, 77.624
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable hydrolase NIT2


Mass: 38277.746 Da / Num. of mol.: 4 / Mutation: C169S
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.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical
ChemComp-KGT / N-(4-carboxy-4-oxobutanoyl)-L-cysteinylglycine


Mass: 306.292 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2O7S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
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: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 80059 / Num. obs: 76148 / % possible obs: 95.1 % / Observed criterion σ(I): 2.38
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 2 % / % possible all: 93.2

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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: 2.04→35.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.288 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22832 3803 5 %RANDOM
Rwork0.18945 ---
all0.2049 76125 --
obs0.1914 72215 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.395 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å2-0.07 Å2
2--1.73 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.04→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9210 0 178 330 9718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.00770.0229576
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.98112974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80951187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99524.247405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.754151595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7321560
X-RAY DIFFRACTIONr_chiral_restr0.0720.21459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217166
X-RAY DIFFRACTIONr_mcbond_it0.3991.55975
X-RAY DIFFRACTIONr_mcangle_it0.75429630
X-RAY DIFFRACTIONr_scbond_it1.11533601
X-RAY DIFFRACTIONr_scangle_it1.8354.53342
LS refinement shellResolution: 2.04→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 245 -
Rwork0.282 4752 -
obs--84.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.04760.1002-0.32510.2324-0.01160.63460.04770.0910.0081-0.0285-0.0039-0.00430.0413-0.087-0.04370.0403-0.0091-0.02280.01770.01150.0383-25.785-22.226.167
20.9181-0.1920.20620.2507-0.11190.3785-0.0271-0.08320.07150.0180.008-0.0089-0.001-0.05470.0190.03770.0068-0.01820.0151-0.01770.06097.115-19.84133.333
31.1629-0.40860.28080.604-0.21350.60130.0246-0.1429-0.05660.0030.0136-0.02620.017-0.0128-0.03820.0264-0.0071-0.02780.02170.01570.050932.208-44.51348.156
41.5528-0.371-0.01591.33180.75690.77890.1123-0.31170.18640.026-0.09630.095-0.0267-0.1021-0.0160.0409-0.0260.05050.0978-0.07580.1212-1.7312.715-8.64
50.0620.02850.02060.07660.11010.1683-0.0116-0.03590.0223-0.00170.0542-0.0209-0.00450.0931-0.04260.06790.005-0.02880.0961-0.02620.0968-3.418-24.95217.629
61.15521.37792.3772.51122.94474.97250.1705-0.1670.06330.08490.0234-0.47680.6157-0.4804-0.19390.4643-0.25090.11340.64160.17140.67530.809-18.62731.141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 306
2X-RAY DIFFRACTION2B4 - 306
3X-RAY DIFFRACTION3C5 - 307
4X-RAY DIFFRACTION4D5 - 306
5X-RAY DIFFRACTION5A401 - 405
6X-RAY DIFFRACTION5B401 - 402
7X-RAY DIFFRACTION5C401 - 403
8X-RAY DIFFRACTION5D401 - 403
9X-RAY DIFFRACTION6A406
10X-RAY DIFFRACTION6B403
11X-RAY DIFFRACTION6C404
12X-RAY DIFFRACTION6D404

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