[English] 日本語
Yorodumi
- PDB-7rll: Crystal structure of ARF3 from Candida albicans in complex with g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rll
TitleCrystal structure of ARF3 from Candida albicans in complex with guanosine-3'-monophosphate-5'-diphosphate
ComponentsArf3p
KeywordsSIGNALING PROTEIN / small GTPase / GTP-BINDING / SIGNAL TRANSDUCTION / structural genomics / CSGID / center for structural genomics of infectious diseases / NIAID / national institute of allergy and infectious diseases
Function / homology
Function and homology information


vesicle-mediated transport / intracellular protein transport / extracellular vesicle / GTPase activity / GTP binding / Golgi apparatus / metal ion binding
Similarity search - Function
Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE / Arf3p
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStogios, P.J. / Michalska, K. / Evdokimova, E. / 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 ARF3 from Candida albicans in complex with guanosine-3'-monophosphate-5'-diphosphate
Authors: Stogios, P.J.
History
DepositionJul 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arf3p
B: Arf3p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9276
Polymers39,8322
Non-polymers1,0954
Water5,945330
1
A: Arf3p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4633
Polymers19,9161
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arf3p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4633
Polymers19,9161
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.958, 75.852, 97.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Arf3p


Mass: 19916.008 Da / Num. of mol.: 2
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: ARF3, orf19.1702, CAALFM_C301470WA / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Gold / References: UniProt: A0A1D8PJ64
#2: Chemical ChemComp-G3D / GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M potassium thiocyanate, 30% (w/v) PEG 2K MME, 2 mM magnesium chloride, 1.5 mM GMP-PCP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 30467 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 34.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.032 / Net I/σ(I): 34.2
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.326 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1471 / CC1/2: 0.921 / Rpim(I) all: 0.428 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1e0s

1e0s


Resolution: 1.9→48.76 Å / SU ML: 0.2208 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.0798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 1966 6.59 %
Rwork0.1849 27868 -
obs0.188 29834 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 66 330 3183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722914
X-RAY DIFFRACTIONf_angle_d1.15263961
X-RAY DIFFRACTIONf_chiral_restr0.0776462
X-RAY DIFFRACTIONf_plane_restr0.0085482
X-RAY DIFFRACTIONf_dihedral_angle_d19.08271085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.31841270.29951780X-RAY DIFFRACTION90.12
1.95-20.28381350.24481868X-RAY DIFFRACTION93.6
2-2.060.26141360.20821913X-RAY DIFFRACTION96.33
2.06-2.130.25091390.21371981X-RAY DIFFRACTION97.56
2.13-2.20.24041360.21831935X-RAY DIFFRACTION97.87
2.2-2.290.25861420.21942014X-RAY DIFFRACTION98.76
2.29-2.390.28471400.21221978X-RAY DIFFRACTION99.06
2.39-2.520.28881400.20371997X-RAY DIFFRACTION99.21
2.52-2.680.27061430.20882022X-RAY DIFFRACTION99.59
2.68-2.890.27161410.20542013X-RAY DIFFRACTION99.72
2.89-3.180.24991450.20022057X-RAY DIFFRACTION99.82
3.18-3.640.23191440.17272057X-RAY DIFFRACTION99.95
3.64-4.580.19611460.14762074X-RAY DIFFRACTION99.82
4.58-48.760.19211520.16662179X-RAY DIFFRACTION99.91
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)
11.345279370183.19500292541-0.2650091121678.749423278981.739880805085.898604523430.1774400650270.1095842456790.71144899765-0.1716846513040.08150478822871.30774500379-1.63946651332-1.0073083041-0.1359687299920.8204715449660.2365877382220.1035921430210.3912404845690.07324723116290.608597985448.5702190560848.6357805761101.448013748
28.75246422692-0.863689754088-4.350777735034.659888472225.001948909426.732512892021.335054873620.1002003134851.63864837840.6710413758440.2213408623231.04059596058-1.05725907187-0.149321250523-1.045570712761.44262936510.02818536219420.3130003507430.4943710941860.03804876844561.093791316957.0138648428257.2794703952111.269991325
37.642320055971.81784749886-1.592183892038.460471743260.4271061667365.734492143880.165112914552-1.596207322720.7722500510371.30769332986-0.3184810973920.0389311935639-1.59638362046-1.070143982710.3489923167451.102652596250.1060472610570.150490355280.61445841301-0.1107332124960.54462730644810.168936837150.3598840003113.826036235
44.261581422190.825282704648-0.3820642766734.53433143423-0.4017401241055.53735225890.19870893914-0.2648885385840.2344879524450.4405709637020.0116373526247-0.132154363725-1.056435038780.26626731144-0.1788768638630.41073635383-0.0136597362946-0.01978188059990.225816644954-0.0477473130270.26355909612919.049231405241.6479706457106.649999655
57.167278747-1.95401495355-0.9753290022616.16116517983-2.885850095573.95808582047-0.00332217278657-0.288443997383-0.513049364020.3214507854170.6018515170440.9721747984770.0987148651099-0.685522740775-0.03033427587450.2746730154430.4120129550320.04866983328490.508523858480.1641221875510.8088653202221.0483671848433.9613221531102.145474491
67.65030158097-3.01606198536-6.747415531195.01060844263.096631187468.43090778279-0.423457554025-1.06322481248-0.329428560751.69424324743-0.153793531191-0.458485585844-0.211436330411.437240521360.418349703431.64186520713-0.142629179058-0.3750213166190.7482690849850.185530035350.67948018294314.176379346212.6733876918126.592831344
79.06486938301-1.32756375009-0.817923938277.570816434641.05719277485.91455991085-0.0301291164115-0.277604030807-0.3254820269310.740874247991-0.1419354673730.03310442286360.102582350291-0.1571769155490.1554231333510.234323809934-0.021570917813-0.001767577975330.179119868670.04729385710910.2399792642729.244902422528.46266034644112.031241436
82.707428319530.8990947685780.3440918889173.811463602030.3450187283751.799094186460.132901648853-0.184001786507-0.08023775371160.597421607805-0.189441914490.1905308243040.238552404282-0.1004104816120.04380555441960.241749584256-0.01460424370620.03007246891770.2975157681440.01824177248640.2326089715652.5467508775711.3654396203109.253495991
91.92030294502-0.328367539998-1.85783052945.447070896121.030895573523.486124001270.0198890814498-0.151011635366-0.00621385242860.499135506125-0.0442800900712-0.3449737671820.08899581939970.2509899787460.02098837704020.169560681294-0.0265634230456-0.09439913984990.2864825590340.03234415763810.25426542000314.436180873120.6970416087109.029923262
103.52067895676-0.336801422444-0.5101710784994.842940377764.230572516863.708977912971.194690615422.34177148002-1.12684386599-1.30641411356-2.268524670631.02111839728-2.56379655007-1.061326540551.023349882351.720646849020.2284121708810.08322956710631.593775767780.0738089514611.013373901243.7423423462223.7939716641127.638412519
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 33 )AA1 - 331 - 33
22chain 'A' and (resid 34 through 51 )AA34 - 5134 - 51
33chain 'A' and (resid 54 through 72 )AA54 - 7254 - 72
44chain 'A' and (resid 73 through 173 )AA73 - 17373 - 173
55chain 'A' and (resid 174 through 175 )AA174 - 175174 - 175
66chain 'B' and (resid -1 through 13 )BC-1 - 131 - 15
77chain 'B' and (resid 14 through 33 )BC14 - 3316 - 35
88chain 'B' and (resid 34 through 122 )BC34 - 12236 - 124
99chain 'B' and (resid 123 through 174 )BC123 - 174125 - 176
1010chain 'B' and (resid 175 through 175 )BC175177

+
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