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- PDB-7elf: Nitrilase-Like Protein Nit2 from Kluyve-romyces lactis -

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Basic information

Entry
Database: PDB / ID: 7elf
TitleNitrilase-Like Protein Nit2 from Kluyve-romyces lactis
ComponentsKLLA0E15247p
KeywordsHYDROLASE / Nitrilase / Nit2
Function / homologyUncharacterised protein family UPF0012, conserved site / Nit1/2, carbon-nitrogen hydrolase domain / Uncharacterized protein family UPF0012 signature. / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / KLLA0E15247p
Function and homology information
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJin, C.W. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019R1A2C4069796 Korea, Republic Of
CitationJournal: Crystals / Year: 2021
Title: Crystal Structure of Nitrilase-Like Protein Nit2 from Kluyveromyces lactis.
Authors: Jin, C.W. / Jin, H.S. / Jeong, B.C. / Cho, D.H. / Chun, H.S. / Kim, W.K. / Chang, J.H.
History
DepositionApr 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KLLA0E15247p
B: KLLA0E15247p
C: KLLA0E15247p
D: KLLA0E15247p


Theoretical massNumber of molelcules
Total (without water)134,5344
Polymers134,5344
Non-polymers00
Water9,782543
1
A: KLLA0E15247p
B: KLLA0E15247p


Theoretical massNumber of molelcules
Total (without water)67,2672
Polymers67,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: KLLA0E15247p
D: KLLA0E15247p


Theoretical massNumber of molelcules
Total (without water)67,2672
Polymers67,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.997, 211.065, 89.372
Angle α, β, γ (deg.)90.00, 112.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

21D-500-

HOH

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Components

#1: Protein
KLLA0E15247p / Nitrilase-like protein 2 (Nit2)


Mass: 33633.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_E15247g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CN52
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 26% w/v polyethylene glycol (PEG 3350), 0.3M Ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 68559 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.991 / Net I/σ(I): 16.96
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 6799 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H5U

4h5u


Resolution: 2.2→45.68 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 1896 2.91 %
Rwork0.1675 --
obs0.1691 65198 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9157 0 0 543 9700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099329
X-RAY DIFFRACTIONf_angle_d0.94112613
X-RAY DIFFRACTIONf_dihedral_angle_d6.5311235
X-RAY DIFFRACTIONf_chiral_restr0.0571431
X-RAY DIFFRACTIONf_plane_restr0.0051629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.30721190.21794017X-RAY DIFFRACTION84
2.25-2.310.29441250.20984189X-RAY DIFFRACTION88
2.31-2.380.26831300.20694287X-RAY DIFFRACTION91
2.38-2.460.3011370.20114382X-RAY DIFFRACTION92
2.46-2.550.24961350.19754441X-RAY DIFFRACTION93
2.55-2.650.25431230.18974447X-RAY DIFFRACTION94
2.65-2.770.24471370.17914526X-RAY DIFFRACTION95
2.77-2.910.21561340.17034624X-RAY DIFFRACTION97
2.91-3.10.24491480.16644648X-RAY DIFFRACTION98
3.1-3.340.20691400.16424724X-RAY DIFFRACTION99
3.34-3.670.20911450.15814696X-RAY DIFFRACTION99
3.67-4.20.17321350.14184761X-RAY DIFFRACTION99
4.2-5.290.20241460.14074754X-RAY DIFFRACTION99
5.29-45.680.21691420.17294806X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.7591 Å / Origin y: 5.2596 Å / Origin z: 20.527 Å
111213212223313233
T0.1102 Å20.0324 Å20.0022 Å2-0.1052 Å20.0198 Å2--0.1598 Å2
L0.0241 °2-0.1502 °2-0.0011 °2--0.3379 °2-0.0217 °2--0.106 °2
S-0.0017 Å °-0.056 Å °-0.0514 Å °-0.0397 Å °0.0109 Å °0.0357 Å °0.0138 Å °0.0216 Å °0.0008 Å °
Refinement TLS groupSelection details: all

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