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- PDB-1vlp: Crystal structure of a putative nicotinate phosphoribosyltransfer... -

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Basic information

Entry
Database: PDB / ID: 1vlp
TitleCrystal structure of a putative nicotinate phosphoribosyltransferase (yor209c, npt1) from saccharomyces cerevisiae at 1.75 A resolution
Componentsnicotinate phosphoribosyltransferase
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


nicotinate nucleotide salvage / nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase activity / NAD+ biosynthetic process via the salvage pathway / rDNA heterochromatin formation / subtelomeric heterochromatin formation / transferase activity / chromosome, telomeric region / nucleus / cytosol
Similarity search - Function
Nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase / Nicotinate phosphoribosyltransferase, N-terminal domain / Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain / Nicotinate phosphoribosyltransferase family / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Nicotinate phosphoribosyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Structure / Year: 2005
Title: The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases.
Authors: Chappie, J.S. / Canaves, J.M. / Han, G.W. / Rife, C.L. / Xu, Q. / Stevens, R.C.
History
DepositionAug 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nicotinate phosphoribosyltransferase
B: nicotinate phosphoribosyltransferase
C: nicotinate phosphoribosyltransferase
D: nicotinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,92015
Polymers204,0524
Non-polymers86811
Water22,8971271
1
A: nicotinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3394
Polymers51,0131
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: nicotinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2685
Polymers51,0131
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: nicotinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2064
Polymers51,0131
Non-polymers1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: nicotinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1082
Polymers51,0131
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.406, 83.103, 107.237
Angle α, β, γ (deg.)97.35, 95.67, 97.99
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
nicotinate phosphoribosyltransferase / NAPRTase


Mass: 51013.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NPT1, YOR209C / Production host: Escherichia coli (E. coli) / References: UniProt: P39683, EC: 2.4.2.11

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Non-polymers , 5 types, 1282 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1271 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.3246.9
22.2945.77TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 3 A MAD DATA FROM ONE CRYSTAL WAS USED TO PHASE THE STRUCTURE. THE INITIAL MODEL WAS THEN EXTENDED AND REBUILT USING ARP/WARP WITH AMPLITUDES FROM A DIFFERENT CRYSTAL THAT DIFFRACTED TO 1.75 A. REFINEMENT WAS AGAINST THE 1.75 A DATA.
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2771vapor diffusion, sitting drop, nanodrop0.06M MES, 0.04M MES_Na, 14% PEG MME 5000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop15% PEG MME 5000, 0.06M MES, 0.04M MES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.110.9686
SYNCHROTRONALS 8.2.221.0332, 0.9798
Detector
TypeIDDetectorDate
ADSC1CCDJan 8, 2004
ADSC2CCDDec 19, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
21.03321
30.97981
ReflectionResolution: 1.75→50 Å / Num. obs: 177740 / % possible obs: 96.81 % / Redundancy: 3.79 % / Biso Wilson estimate: 28.97 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.09
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.64 / Num. unique all: 16630 / % possible all: 90.05

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHARPphasing
REFMAC5.2.0005refinement
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→48.24 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.444 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20962 8921 5 %RANDOM
Rwork0.16964 ---
obs0.17163 168817 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20.01 Å2-0.03 Å2
2--0.04 Å20.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13317 0 47 1271 14635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213808
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212289
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.95518690
X-RAY DIFFRACTIONr_angle_other_deg0.859328770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16851669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48324.72625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.068152466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7561548
X-RAY DIFFRACTIONr_chiral_restr0.0940.22071
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022743
X-RAY DIFFRACTIONr_nbd_refined0.2150.22844
X-RAY DIFFRACTIONr_nbd_other0.1760.211954
X-RAY DIFFRACTIONr_nbtor_other0.0850.27300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2900
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.2118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.253
X-RAY DIFFRACTIONr_mcbond_it2.1638545
X-RAY DIFFRACTIONr_mcbond_other0.55833379
X-RAY DIFFRACTIONr_mcangle_it2.854513599
X-RAY DIFFRACTIONr_scbond_it4.73685976
X-RAY DIFFRACTIONr_scangle_it6.54115090
X-RAY DIFFRACTIONr_nbtor_refined0.1820.26720
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 570 5.18 %
Rwork0.234 10442 -
obs--80.87 %
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)
10.53580.07360.12510.29010.24250.5819-0.00370.03180.01620.00250.0394-0.04070.04150.0377-0.0357-0.05230.0113-0.0164-0.09040.0059-0.075828.05747.1755-47.3839
20.5241-0.23660.0880.75520.25880.469-0.0842-0.0330.06920.06880.0746-0.0597-0.1227-0.0490.00960.04580.02190.023-0.06390.0075-0.01141.047643.6244-34.5756
30.643-0.11850.40040.4151-0.03460.7522-0.0077-0.01320.0126-0.00530.01240.0187-0.0209-0.075-0.0047-0.1547-0.01180.0345-0.07550.0181-0.1221-1.7695-0.8488-1.8235
40.55670.29210.38820.97890.3410.8260.0105-0.016-0.06370.08440.0572-0.0670.04520.0108-0.0676-0.0633-0.02840.0176-0.04710.01140.0129-20.238954.5574-83.0286
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-2 - 41510 - 427
21AE5001
32BB1 - 41913 - 431
42BF5001
53CC-1 - 41611 - 428
63CG5001
74DD0 - 41512 - 427
84DH5001

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