[English] 日本語
Yorodumi
- PDB-7rh8: Crystal structure of Fur1p from Candida albicans, in complex with UTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rh8
TitleCrystal structure of Fur1p from Candida albicans, in complex with UTP
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / fur1 / drug target / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / national institute of allergy and infectious diseases
Function / homologypyrimidine-containing compound salvage / Uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / fungal biofilm matrix / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / URIDINE 5'-TRIPHOSPHATE / Uracil phosphoribosyltransferase
Function and homology information
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsStogios, P.J. / Skarina, T. / Kim, Y. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of Fur1p from Candida albicans, in complex with UTP
Authors: Stogios, P.J.
History
DepositionJul 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9912
Polymers24,5071
Non-polymers4841
Water5,819323
1
A: Uracil phosphoribosyltransferase
hetero molecules

A: Uracil phosphoribosyltransferase
hetero molecules

A: Uracil phosphoribosyltransferase
hetero molecules

A: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9648
Polymers98,0274
Non-polymers1,9374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_445-y-1,-x-1,-z+1/31
Buried area17140 Å2
ΔGint-67 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.967, 145.967, 51.014
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

21A-493-

HOH

31A-529-

HOH

41A-592-

HOH

51A-613-

HOH

61A-624-

HOH

71A-630-

HOH

81A-636-

HOH

-
Components

#1: Protein Uracil phosphoribosyltransferase


Mass: 24506.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: FUR1, orf19.2640, CAALFM_C503390CA / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Gold / References: UniProt: Q59QT3
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25% (w/v) PEG3350, 0.2 M NaCl, 0.1 M sodium citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97869 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 35544 / % possible obs: 98 % / Redundancy: 13.4 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.022 / Net I/σ(I): 29.73
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1496 / CC1/2: 0.949 / Rpim(I) all: 0.262 / % possible all: 84.3

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JLS

1jls


Resolution: 1.69→47.78 Å / SU ML: 0.1571 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 1776 5 %RANDOM
Rwork0.1615 33750 --
obs0.1631 35526 97.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1 Å2
Refinement stepCycle: LAST / Resolution: 1.69→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 29 323 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01891734
X-RAY DIFFRACTIONf_angle_d1.70852341
X-RAY DIFFRACTIONf_chiral_restr0.1173263
X-RAY DIFFRACTIONf_plane_restr0.0194295
X-RAY DIFFRACTIONf_dihedral_angle_d15.1333677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.2861170.24022215X-RAY DIFFRACTION85.05
1.74-1.790.26381330.21412551X-RAY DIFFRACTION98.03
1.79-1.840.20691360.19432580X-RAY DIFFRACTION98.55
1.84-1.910.22061350.192581X-RAY DIFFRACTION98.76
1.91-1.990.20721360.16652576X-RAY DIFFRACTION98.51
1.99-2.080.18291360.16432573X-RAY DIFFRACTION98.8
2.08-2.190.20721370.15712621X-RAY DIFFRACTION99.35
2.19-2.320.16571390.15912633X-RAY DIFFRACTION99.18
2.32-2.50.20171360.15932593X-RAY DIFFRACTION98.7
2.5-2.750.22771400.16452654X-RAY DIFFRACTION99.43
2.75-3.150.18531390.15922642X-RAY DIFFRACTION98.72
3.15-3.970.1481430.1392721X-RAY DIFFRACTION99.9
3.97-47.780.20011490.16112810X-RAY DIFFRACTION97.72
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)
10.9157797882510.1149309608950.5805877088222.7239859986-0.1025729833452.677743726290.0556670689296-0.02806846860480.01435669958080.0318505141932-0.0392806609933-0.00183804516841-0.1679196346180.179994466018-0.007368270775450.07732756069230.01956371283090.01025055394990.188537780532-0.02212574157980.142795801197-22.7006264954-52.966517282915.9301890913
23.53365282499-1.886670115950.2371544025773.14834437887-0.9495738844221.601650939770.0136760373262-0.0922985028845-0.1622902492240.0345649871573-0.033661242449-0.1689432822850.04055708307260.214554180954-0.007842200502970.127676401307-0.00392629156637-0.01911696166120.153211056052-0.06323573681220.132832467712-24.7954007523-56.6395828341-2.70773260036
31.264117636830.382563982826-0.9291683089430.9563578057410.4322020303771.692308777680.00195467525605-0.20524272551-0.172288539336-0.01849996412250.0175095162227-0.2232618519890.1096843382790.585878314404-0.06272742720970.1349390944330.07027603417360.005571920138250.3111431097440.005278357586460.229934846969-10.2320825556-61.9132085318.56205099459
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 55 )7 - 551 - 49
22chain 'A' and (resid 56 through 112 )56 - 11250 - 106
33chain 'A' and (resid 113 through 218 )113 - 218107 - 212

+
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