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- PDB-6kua: Crystal structure of the nicotinamidase SaPncA from Staphylococcu... -

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Basic information

Entry
Database: PDB / ID: 6kua
TitleCrystal structure of the nicotinamidase SaPncA from Staphylococcus aureus
ComponentsCysteine hydrolase
KeywordsHYDROLASE / Nicotinamidase / SaPncA / Staphylococcus aureus
Function / homology
Function and homology information


ureidoacrylate amidohydrolase / nicotinamidase activity / nicotinamidase / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
Similarity search - Function
Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cysteine hydrolase / Cysteine hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 Å
AuthorsShang, F. / Lan, J. / Liu, W. / Xu, Y. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31200556 China
National Natural Science Foundation of China21272031 China
CitationJournal: To Be Published
Title: Crystal structure of the nicotinamidase SaPncA from Staphylococcus aureus
Authors: Shang, F. / Lan, J. / Wang, L. / Xu, Y. / Chen, Y.
History
DepositionAug 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine hydrolase
B: Cysteine hydrolase
C: Cysteine hydrolase
D: Cysteine hydrolase
E: Cysteine hydrolase
F: Cysteine hydrolase
G: Cysteine hydrolase
H: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,26515
Polymers169,8088
Non-polymers4587
Water12,701705
1
A: Cysteine hydrolase
B: Cysteine hydrolase
C: Cysteine hydrolase
D: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1007
Polymers84,9044
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Cysteine hydrolase
F: Cysteine hydrolase
G: Cysteine hydrolase
H: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1658
Polymers84,9044
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.019, 89.019, 210.694
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein
Cysteine hydrolase / Isochorismatase / Isochorismatase family protein / Nicotinamidase


Mass: 21225.938 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: W8TV24, UniProt: A0A0D1IA98*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, nicotinamidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M sodium citrate tribasic dihydrate pH 5.6, 30% (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979462 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979462 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 93388 / % possible obs: 99.4 % / Redundancy: 8.1 % / Biso Wilson estimate: 26.1 Å2 / Rsym value: 0.101 / Net I/σ(I): 29.37
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 4524 / Rsym value: 0.37

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZN8

5zn8


Resolution: 2.104→40.4 Å / SU ML: 0.2288 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.4748
RfactorNum. reflection% reflection
Rfree0.2272 4592 4.99 %
Rwork0.1801 --
obs0.1825 92082 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.93 Å2
Refinement stepCycle: LAST / Resolution: 2.104→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10243 0 7 705 10955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007610479
X-RAY DIFFRACTIONf_angle_d0.840914179
X-RAY DIFFRACTIONf_chiral_restr0.05291555
X-RAY DIFFRACTIONf_plane_restr0.00511821
X-RAY DIFFRACTIONf_dihedral_angle_d7.56626094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1034-2.12730.26571090.23632506261583
2.1273-2.15230.25231530.21932747290093
2.1523-2.17860.29031810.21122870305196
2.1786-2.20610.26941590.20592823298296
2.2061-2.23520.24781550.20242928308397
2.2352-2.26580.2251530.21732828298195
2.2658-2.29810.26741590.2092878303797
2.2981-2.33240.24611350.20222886302197
2.3324-2.36890.26111520.19852889304197
2.3689-2.40770.26471390.19382971311097
2.4077-2.44920.23451600.18482876303697
2.4492-2.49380.22081830.18882902308597
2.4938-2.54170.22291470.1862937308498
2.5417-2.59360.24311430.18662914305798
2.5936-2.650.26461540.1872936309098
2.65-2.71160.23561610.17992936309798
2.7116-2.77940.22691320.18622956308898
2.7794-2.85450.2731570.18812939309698
2.8545-2.93850.25171640.17832932309699
2.9385-3.03330.23921590.17392920307997
3.0333-3.14170.22251550.18222927308298
3.1417-3.26740.26611400.19113019315999
3.2674-3.41610.24471550.190330113166100
3.4161-3.59610.19871450.177929723117100
3.5961-3.82120.21011650.162830033168100
3.8212-4.1160.18231630.150829593122100
4.116-4.52970.19261520.144130253177100
4.5297-5.1840.1921590.149330103169100
5.184-6.52680.2391380.19282978311699
6.5268-40.40330.21241650.18933012317799

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