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- PDB-9leh: nitrile synthetase ArtA -

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Basic information

Entry
Database: PDB / ID: 9leh
Titlenitrile synthetase ArtA
Componentsnitrile synthetase
KeywordsBIOSYNTHETIC PROTEIN / nitrile synthetase / argininosuccinate synthetase like enzyme / nitrile group / complex.
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesPenicillium aurantiogriseum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsMa, H.L. / Zhang, K.K.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271358 China
Other governmentLZR202211060073
Other governmentZR2024QC065
CitationJournal: To Be Published
Title: Crystal structure of nitrile synthetase ArtA in complex with ATP
Authors: Ma, H.L. / Zhang, K.K.
History
DepositionJan 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nitrile synthetase
B: nitrile synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,93312
Polymers95,7702
Non-polymers1,16310
Water9,458525
1
A: nitrile synthetase
B: nitrile synthetase
hetero molecules

A: nitrile synthetase
B: nitrile synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,86624
Polymers191,5404
Non-polymers2,32520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area15210 Å2
ΔGint-51 kcal/mol
Surface area57490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.757, 105.035, 85.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-696-

HOH

21A-732-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein nitrile synthetase


Mass: 47885.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium aurantiogriseum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 535 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: succinic acid, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.81→85.41 Å / Num. obs: 75408 / % possible obs: 99.83 % / Redundancy: 6.7 % / CC1/2: 0.985 / R split: 0.1 / Net I/σ(I): 4.3
Reflection shellResolution: 1.81→5.71 Å / Rmerge(I) obs: 0.163 / Num. unique obs: 75408 / CC1/2: 0.985 / Rrim(I) all: 0.194 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
autoPXdata reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→66.26 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 3747 4.98 %
Rwork0.1933 --
obs0.1953 75230 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→66.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5992 0 15 525 6532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056146
X-RAY DIFFRACTIONf_angle_d0.7828336
X-RAY DIFFRACTIONf_dihedral_angle_d17.627849
X-RAY DIFFRACTIONf_chiral_restr0.05935
X-RAY DIFFRACTIONf_plane_restr0.0051069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.35131410.33372561X-RAY DIFFRACTION99
1.83-1.850.32861550.32682593X-RAY DIFFRACTION99
1.85-1.880.34571390.29832587X-RAY DIFFRACTION100
1.88-1.910.31591350.30692614X-RAY DIFFRACTION100
1.91-1.930.35551440.28382603X-RAY DIFFRACTION100
1.93-1.960.2841460.26762609X-RAY DIFFRACTION100
1.96-20.28691190.2532631X-RAY DIFFRACTION100
2-2.030.24691250.24272642X-RAY DIFFRACTION100
2.03-2.070.26711640.23642610X-RAY DIFFRACTION100
2.07-2.110.25951330.22282639X-RAY DIFFRACTION100
2.11-2.150.27771510.22112608X-RAY DIFFRACTION100
2.15-2.20.26041360.20832640X-RAY DIFFRACTION100
2.2-2.250.2531230.20132641X-RAY DIFFRACTION100
2.25-2.310.21961410.19652646X-RAY DIFFRACTION100
2.31-2.370.20981320.19692621X-RAY DIFFRACTION100
2.37-2.440.25091340.19212678X-RAY DIFFRACTION100
2.44-2.520.25511320.19572634X-RAY DIFFRACTION100
2.52-2.610.23771430.19792634X-RAY DIFFRACTION100
2.61-2.710.25231470.20072652X-RAY DIFFRACTION100
2.71-2.830.27381200.19962687X-RAY DIFFRACTION100
2.83-2.980.23521190.19542651X-RAY DIFFRACTION100
2.98-3.170.24571470.19192671X-RAY DIFFRACTION100
3.17-3.410.2241320.18912673X-RAY DIFFRACTION100
3.41-3.760.19681610.16742686X-RAY DIFFRACTION100
3.76-4.30.16291350.15142705X-RAY DIFFRACTION100
4.3-5.420.21591440.15782738X-RAY DIFFRACTION100
5.42-66.260.23591490.1872829X-RAY DIFFRACTION99
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)
11.3552-0.1447-0.14032.0662-0.03573.08970.04270.38310.1752-0.33590.1463-0.094-0.39980.3613-0.1190.3293-0.03590.03330.2971-0.0240.2769-2.202430.8237-31.236
20.35220.0690.12951.01160.86372.78990.04330.09770.0513-0.19360.0885-0.0277-0.07220.2039-0.08540.17830.0011-0.00280.2117-0.01470.2348-5.708530.6551-18.3644
31.0883-0.2179-0.43130.88850.24391.37240.0150.0201-0.1204-0.06370.0523-0.00870.06080.053-0.04970.19870.0085-0.02390.1533-0.01030.2328-12.433733.49731.4401
41.2589-0.7034-0.21591.23320.16931.5425-0.0531-0.4933-0.23710.22010.0922-0.01320.25410.0009-0.02420.28360.0191-0.02430.32470.0470.2202-13.462832.551224.3053
51.2172-0.6035-0.18511.62430.7282.5614-0.132-0.2877-0.00930.37390.1103-0.02680.060.0749-0.03040.27160.0156-0.02340.2570.00070.2275-22.211355.857635.5363
61.09670.0912-0.13870.97540.2761.15350.03630.01170.0117-0.0927-0.02490.0423-0.0795-0.1044-0.00420.17670.0259-0.0030.17270.00020.2012-22.351748.14387.4786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 355 )
4X-RAY DIFFRACTION4chain 'A' and (resid 356 through 393 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 208 )
6X-RAY DIFFRACTION6chain 'B' and (resid 209 through 393 )

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