[English] 日本語
Yorodumi
- PDB-1vlp: Crystal structure of a putative nicotinate phosphoribosyltransfer... -

+
Open data


ID or keywords:

Loading...

-
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


Nicotinamide salvaging / nicotinate nucleotide salvage / subtelomeric heterochromatin formation => GO:0031509 / nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase activity / NAD salvage / nicotinate-nucleotide diphosphorylase (carboxylating) activity / rDNA heterochromatin formation / Neutrophil degranulation / chromosome, telomeric region ...Nicotinamide salvaging / nicotinate nucleotide salvage / subtelomeric heterochromatin formation => GO:0031509 / nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase activity / NAD salvage / nicotinate-nucleotide diphosphorylase (carboxylating) activity / rDNA heterochromatin formation / Neutrophil degranulation / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 1282 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


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


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 / Ethylene glycol


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more