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- PDB-5xgs: Crystal structure of human WBSCR16 -

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Basic information

Entry
Database: PDB / ID: 5xgs
TitleCrystal structure of human WBSCR16
ComponentsRCC1-like G exchanging factor-like protein
KeywordsUNKNOWN FUNCTION / RCC1-like protein / beta-propeller / mitochondria
Function / homology
Function and homology information


positive regulation of mitochondrial translation / mitochondrial fusion / guanyl-nucleotide exchange factor activity / mitochondrial membrane / mitochondrial inner membrane / rRNA binding / GTP binding / RNA binding
Similarity search - Function
: / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II
Similarity search - Domain/homology
RCC1-like G exchanging factor-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKoyama, M. / Sasaki, N. / Matsuura, Y.
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structure of human WBSCR16, an RCC1-like protein in mitochondria
Authors: Koyama, M. / Sasaki, T. / Sasaki, N. / Matsuura, Y.
History
DepositionApr 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RCC1-like G exchanging factor-like protein
B: RCC1-like G exchanging factor-like protein


Theoretical massNumber of molelcules
Total (without water)91,8412
Polymers91,8412
Non-polymers00
Water10,773598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area31570 Å2
Unit cell
Length a, b, c (Å)111.020, 54.550, 140.473
Angle α, β, γ (deg.)90.000, 95.820, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein RCC1-like G exchanging factor-like protein / RCC1 like / Williams-Beuren syndrome chromosomal region 16 protein


Mass: 45920.742 Da / Num. of mol.: 2 / Fragment: UNP residues 32-464
Source method: isolated from a genetically manipulated source
Details: This is human WBSCR16 residues 32-464, in which residues 146-153 are replaced with two glycine residues.
Source: (gene. exp.) Homo sapiens (human) / Gene: RCC1L, WBSCR16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96I51
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidues 146-153 are replaced with two glycine residues.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→34.94 Å / Num. obs: 56417 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.103 / Rrim(I) all: 0.201 / Net I/σ(I): 6.5 / Num. measured all: 214273 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.053.80.840.5310.5020.9898.3
8.94-34.943.50.0620.9950.0390.07398

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.3.11data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
CRANKphasing
RefinementMethod to determine structure: MAD / Resolution: 2→34.937 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.94
RfactorNum. reflection% reflection
Rfree0.2182 2822 5 %
Rwork0.1796 --
obs0.1815 56397 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.11 Å2 / Biso mean: 20.0099 Å2 / Biso min: 6.83 Å2
Refinement stepCycle: final / Resolution: 2→34.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6016 0 0 598 6614
Biso mean---24.32 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026160
X-RAY DIFFRACTIONf_angle_d0.5318358
X-RAY DIFFRACTIONf_chiral_restr0.047901
X-RAY DIFFRACTIONf_plane_restr0.0031101
X-RAY DIFFRACTIONf_dihedral_angle_d3.9823575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03450.31551390.2772632277198
2.0345-2.07150.27921500.25722632278299
2.0715-2.11130.28691450.23912583272897
2.1113-2.15440.27571270.222826802807100
2.1544-2.20120.2691300.21172641277198
2.2012-2.25240.22761350.21312679281499
2.2524-2.30880.25271480.20312634278298
2.3088-2.37120.25471430.2052663280698
2.3712-2.44090.25651430.205826822825100
2.4409-2.51970.25261410.19692632277399
2.5197-2.60970.23661230.18952685280899
2.6097-2.71420.24861630.185426932856100
2.7142-2.83760.23571370.18672658279599
2.8376-2.98720.21211500.1862677282799
2.9872-3.17420.21791450.180427122857100
3.1742-3.41910.20711470.16272686283399
3.4191-3.76280.19221440.155927032847100
3.7628-4.30640.14691370.134927242861100
4.3064-5.42240.16941290.130927722901100
5.4224-34.94230.16961460.15752807295399

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