2QU8 | pdb_00002qu8

Crystal structure of putative nucleolar GTP-binding protein 1 PFF0625w from Plasmodium falciparum

PDB DOI: https://doi.org/10.2210/pdb2QU8/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-08-03 Released: 2007-08-28
Deposition Author(s): 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.264 (Depositor), 0.250 (DCC)
R-Value Work:
0.223 (Depositor), 0.220 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of putative nucleolar GTP-binding protein 1 PFF0625w from Plasmodium falciparum.

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.

To be published.

Macromolecule Content

Total Structure Weight: 25.96 kDa
Atom Count: 1,612
Modelled Residue Count: 194
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative nucleolar GTP-binding protein 1	A	228	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PFF0625w
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.264 (Depositor), 0.250 (DCC)
R-Value Work: 0.223 (Depositor), 0.220 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.377	α = 90
b = 77.162	β = 90
c = 40.196	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SHELXD	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-08-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-08-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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Crystal structure of putative nucleolar GTP-binding protein 1 PFF0625w from Plasmodium falciparum

Crystal structure of putative nucleolar GTP-binding protein 1 PFF0625w from Plasmodium falciparum.

Entity ID: 1

Entity Groups

Sequence Annotations

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