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- PDB-5xqh: Crystal structure of truncated human Rogdi -

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Basic information

Entry
Database: PDB / ID: 5xqh
TitleCrystal structure of truncated human Rogdi
ComponentsProtein rogdi homolog
KeywordsCELL CYCLE / Rogdi / Kohlschutter-Tonz syndrome
Function / homology
Function and homology information


RAVE complex / pH reduction / enamel mineralization / locomotion / neuromuscular process / bone mineralization / locomotor rhythm / odontogenesis of dentin-containing tooth / hemopoiesis / neurogenesis ...RAVE complex / pH reduction / enamel mineralization / locomotion / neuromuscular process / bone mineralization / locomotor rhythm / odontogenesis of dentin-containing tooth / hemopoiesis / neurogenesis / hippocampal mossy fiber to CA3 synapse / brain development / memory / synaptic vesicle / nuclear envelope / perikaryon / gene expression / response to xenobiotic stimulus / axon / positive regulation of cell population proliferation / dendrite
Similarity search - Function
RAVE subunit 2/Rogdi / Rogdi leucine zipper containing protein
Similarity search - Domain/homology
Protein rogdi homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsLee, H. / Lee, C.
CitationJournal: Sci Rep / Year: 2017
Title: The crystal structure of human Rogdi provides insight into the causes of Kohlschutter-Tonz Syndrome
Authors: Lee, H. / Jeong, H. / Choe, J. / Jun, Y. / Lim, C. / Lee, C.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Protein rogdi homolog


Theoretical massNumber of molelcules
Total (without water)30,3281
Polymers30,3281
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.364, 114.695, 44.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein rogdi homolog


Mass: 30328.027 Da / Num. of mol.: 1 / Fragment: UNP residues 11-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROGDI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9GZN7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 4000, 100mM MES pH 6.5, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 39509 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 49.8
Reflection shellHighest resolution: 2.04 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data processing
Cootmodel building
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.04→34.57 Å / Cross valid method: FREE R-VALUE
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.247 --
Rwork0.2 --
obs-39509 99.82 %
Refinement stepCycle: LAST / Resolution: 2.04→34.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 0 166 1929

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