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- PDB-2h0r: Structure of the Yeast Nicotinamidase Pnc1p -

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Basic information

Entry
Database: PDB / ID: 2h0r
TitleStructure of the Yeast Nicotinamidase Pnc1p
ComponentsNicotinamidase
KeywordsHYDROLASE / nicotinamidase / NAD+ salvage pathway
Function / homology
Function and homology information


nicotinate nucleotide salvage / negative regulation of DNA amplification / nicotinamidase activity / nicotinamidase / rDNA heterochromatin formation / subtelomeric heterochromatin formation / peroxisome / chromosome, telomeric region / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIRAS / Resolution: 2.9 Å
AuthorsTaylor, A.B. / Hu, G. / Hart, P.J. / McAlister-Henn, L.
CitationJournal: Arch.Biochem.Biophys. / Year: 2007
Title: Crystal structure of the yeast nicotinamidase Pnc1p.
Authors: Hu, G. / Taylor, A.B. / McAlister-Henn, L. / Hart, P.J.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 14, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Nicotinamidase
B: Nicotinamidase
C: Nicotinamidase
D: Nicotinamidase
E: Nicotinamidase
F: Nicotinamidase
G: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,67014
Polymers175,2127
Non-polymers4587
Water0
1
A: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0962
Polymers25,0301
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0962
Polymers25,0301
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0962
Polymers25,0301
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0962
Polymers25,0301
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0962
Polymers25,0301
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0962
Polymers25,0301
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0962
Polymers25,0301
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)302.040, 302.040, 112.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 1 - 216 / Label seq-ID: 1 - 216

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG

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Components

#1: Protein
Nicotinamidase / / Nicotine deamidase / NAMase


Mass: 25030.332 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: MMYO11 / References: UniProt: P53184, nicotinamidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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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: 5.62 Å3/Da / Density % sol: 78.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.9M sodium citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM11.0332
SYNCHROTRONAPS 19-BM21.0719
SYNCHROTRONALS 8.2.131.1401,1.1405,1.1390
SYNCHROTRONALS 8.2.141.8
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDFeb 11, 2004
CUSTOM-MADE2CCDAug 19, 2004
ADSC QUANTUM 2103CCDNov 23, 2004
ADSC QUANTUM 2104CCDNov 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21.07191
31.14011
41.14051
51.1391
61.81
ReflectionResolution: 2.9→50 Å / Num. all: 84498 / Num. obs: 84498 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 71.5 Å2 / Rsym value: 0.07 / Net I/σ(I): 21
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 8439 / Rsym value: 0.559 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD, MIRAS / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 22.497 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21997 4226 5 %RANDOM
Rwork0.18912 ---
all0.19066 80251 --
obs0.19066 80251 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.431 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12341 0 7 0 12348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212663
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.93617227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57751505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.624.713609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.969152205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2181549
X-RAY DIFFRACTIONr_chiral_restr0.0960.21911
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029576
X-RAY DIFFRACTIONr_nbd_refined0.2160.25955
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2419
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.23
X-RAY DIFFRACTIONr_mcbond_it0.4191.57686
X-RAY DIFFRACTIONr_mcangle_it0.778212425
X-RAY DIFFRACTIONr_scbond_it1.31935594
X-RAY DIFFRACTIONr_scangle_it2.1324.54802
Refine LS restraints NCS

Ens-ID: 1 / Number: 1763 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.395
2Bloose positional0.365
3Cloose positional0.355
4Dloose positional0.375
5Eloose positional0.495
6Floose positional0.495
7Gloose positional0.375
1Aloose thermal3.2110
2Bloose thermal2.3210
3Cloose thermal1.7610
4Dloose thermal2.2910
5Eloose thermal1.9110
6Floose thermal1.9610
7Gloose thermal1.8810
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 308 -
Rwork0.259 5957 -
obs-6265 99.97 %
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)
11.3489-0.07720.31712.6394-1.28523.6878-0.09140.0393-0.0805-0.27810.03630.07010.1824-0.24280.0551-0.52630.0743-0.0199-0.4207-0.0431-0.5184-44.0149267.4255.9927
23.3780.3498-0.63942.537-0.76563.0905-0.0154-0.46860.45840.4291-0.0634-0.4138-0.23190.57840.0788-0.44710.0510.0048-0.1055-0.0472-0.292-10.5656267.905714.9839
32.2453-0.7722-0.12132.4398-0.11295.3552-0.2238-0.34760.62850.31270.1037-0.2574-0.96190.14130.1201-0.12430.1592-0.0793-0.2744-0.1429-0.2438-52.7329298.527217.584
42.8765-0.5636-0.40734.29620.19853.4075-0.15070.7025-0.3217-0.5967-0.0177-0.18590.31010.2230.1684-0.24590.22570.10590.2511-0.0446-0.18511.9042250.1705-11.8303
53.10340.20170.19112.31960.02492.6422-0.053-0.5228-0.30720.67610.0057-0.29210.388-0.04020.04740.13390.51480.07090.63-0.04540.387827.6001234.48055.0548
61.7369-0.20780.27223.29480.4063.6234-0.15510.47010.7835-0.35860.1126-0.0583-0.7291-0.03140.04250.13660.4510.02940.56730.04460.550150.9712233.6467-20.2325
73.7355-0.05210.88112.6338-0.32564.4693-0.0636-0.0824-0.48250.24430.05210.61060.5029-0.73910.0114-0.10260.28420.1130.3063-0.08040.037765.6205203.7313-11.5816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 216
2X-RAY DIFFRACTION2B1 - 216
3X-RAY DIFFRACTION3C1 - 216
4X-RAY DIFFRACTION4D1 - 216
5X-RAY DIFFRACTION5E1 - 216
6X-RAY DIFFRACTION6F1 - 216
7X-RAY DIFFRACTION7G1 - 216

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