[English] 日本語
Yorodumi
- PDB-2qu8: Crystal structure of putative nucleolar GTP-binding protein 1 PFF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qu8
TitleCrystal structure of putative nucleolar GTP-binding protein 1 PFF0625w from Plasmodium falciparum
ComponentsPutative nucleolar GTP-binding protein 1
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GTPase / malaria / plasmodium falciparum / Structural Genomics Consortium / SGC
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GUANOSINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsWernimont, A.K. / Lew, J. / Lin, Y.H. / Kozieradzki, I. / Zhao, Y. / Ravichandran, M. / Shapiro, M. / Bochkarev, A. / Edwards, A.M. / Arrowsmith, C.H. ...Wernimont, A.K. / Lew, J. / Lin, Y.H. / Kozieradzki, I. / Zhao, Y. / Ravichandran, M. / Shapiro, M. / Bochkarev, A. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Hui, R. / Qiu, W. / Sukumar, D. / Hassanali, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of putative nucleolar GTP-binding protein 1 PFF0625w from Plasmodium falciparum.
Authors: Wernimont, A.K. / Lew, J. / Lin, Y.H. / Zhao, Y. / Kozieradzki, I. / Ravichandran, M. / Shapiro, M. / Bochkarev, A. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Hui, R. ...Authors: Wernimont, A.K. / Lew, J. / Lin, Y.H. / Zhao, Y. / Kozieradzki, I. / Ravichandran, M. / Shapiro, M. / Bochkarev, A. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Hui, R. / Qiu, W. / Sukumar, D. / Hassanali, A.
History
DepositionAug 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Putative nucleolar GTP-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9642
Polymers25,5211
Non-polymers4431
Water1,29772
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.377, 77.162, 40.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Putative nucleolar GTP-binding protein 1


Mass: 25521.195 Da / Num. of mol.: 1 / Fragment: Residues 166-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFF0625w / Plasmid: p15-TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q6LFE0
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal
ID
1
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop6.528% PEG 2000 MME, 0.1 M Bis-Tris pH 6.5, 1 mM GDP, 2 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop5.228% PEG 3350, 0.2 M NaCl, 0.1 M Na Cacodylate pH 5.2, 1 mM GDP, 2 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97937
ROTATING ANODERIGAKU FR-E+ DW21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 10, 2007
RIGAKU RAXIS IV2IMAGE PLATEMay 3, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
21.54181
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 7.4 / Number: 86347 / Rmerge(I) obs: 0.093 / Χ2: 1.26 / D res high: 2 Å / D res low: 40 Å / Num. obs: 12457 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.314099.510.0492.2386.4
3.424.3110010.0642.0736.9
2.993.4210010.0771.3017.1
2.712.9910010.1081.1227.2
2.522.7110010.1361.0257.2
2.372.5210010.1690.957.2
2.252.3710010.2230.9327.2
2.152.2510010.2741.0597.1
2.072.1510010.3450.8526.9
22.0799.310.4010.9826.2
ReflectionResolution: 2.01→50 Å / Num. all: 12175 / Num. obs: 12175 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Rsym value: 0.041 / Χ2: 1.221 / Net I/σ(I): 11.9
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.25 / Num. unique all: 1181 / Rsym value: 0.301 / Χ2: 0.816 / % possible all: 100

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→32.72 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.668 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 580 4.8 %RANDOM
Rwork0.223 ---
all0.225 12151 --
obs0.225 12139 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.58 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.01→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 28 72 1612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221560
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9922112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.645190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18926.40664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96815290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.388153
X-RAY DIFFRACTIONr_chiral_restr0.0730.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021102
X-RAY DIFFRACTIONr_nbd_refined0.1930.2732
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.28
X-RAY DIFFRACTIONr_mcbond_it0.5781.5994
X-RAY DIFFRACTIONr_mcangle_it1.02521564
X-RAY DIFFRACTIONr_scbond_it1.1223637
X-RAY DIFFRACTIONr_scangle_it1.8034.5548
LS refinement shellResolution: 2.01→2.065 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 43 -
Rwork0.273 818 -
all-861 -
obs-614 100 %

+
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