2RHD | pdb_00002rhd

Crystal structure of Cryptosporidium parvum small GTPase RAB1A

PDB DOI: https://doi.org/10.2210/pdb2RHD/pdb

Classification: NUCLEOTIDE BINDING PROTEIN
Organism(s): Cryptosporidium parvum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-09 Released: 2007-10-23
Deposition Author(s): Dong, A., Xu, X., Lew, J., Lin, Y.H., Khuu, C., Sun, X., Qiu, W., Kozieradzki, I., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Sukumar, D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.209 (Depositor), 0.202 (DCC)
R-Value Work:
0.180 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Cryptosporidium parvum small GTPase RAB1A.

Dong, A., Xu, X., Lew, J., Lin, Y.H., Khuu, C., Sun, X., Qiu, W., Kozieradzki, I., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Sukumar, D.

To be published.

Macromolecule Content

Total Structure Weight: 20.51 kDa
Atom Count: 1,509
Modeled Residue Count: 164
Deposited Residue Count: 175
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small GTP binding protein rab1a	A	175	Cryptosporidium parvum	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.209 (Depositor), 0.202 (DCC)
R-Value Work: 0.180 (Depositor), 0.179 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.385	α = 90
b = 107.385	β = 90
c = 45.226	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description