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- PDB-5xqi: Crystal structure of full-length human Rogdi -

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Basic information

Entry
Database: PDB / ID: 5xqi
TitleCrystal structure of full-length 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein rogdi homolog
B: Protein rogdi homolog
C: Protein rogdi homolog
D: Protein rogdi homolog


Theoretical massNumber of molelcules
Total (without water)129,7374
Polymers129,7374
Non-polymers00
Water1,910106
1
A: Protein rogdi homolog
B: Protein rogdi homolog
C: Protein rogdi homolog
D: Protein rogdi homolog

A: Protein rogdi homolog
B: Protein rogdi homolog
C: Protein rogdi homolog
D: Protein rogdi homolog

A: Protein rogdi homolog
B: Protein rogdi homolog
C: Protein rogdi homolog
D: Protein rogdi homolog


Theoretical massNumber of molelcules
Total (without water)389,21112
Polymers389,21112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area37980 Å2
ΔGint-245 kcal/mol
Surface area143410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.372, 169.372, 220.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Protein rogdi homolog


Mass: 32434.248 Da / Num. of mol.: 4
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.: 106 / Source method: isolated from a natural source / Formula: H2O

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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: 4.71 Å3/Da / Density % sol: 73.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2M sodium chloride, 130mM magnesium chloride, 100mM TRIS pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 57790 / % possible obs: 99.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 44.6
Reflection shellHighest resolution: 2.8 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data processing
PHENIXphasing
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XQH

5xqh


Resolution: 2.8→36.17 Å / Cross valid method: FREE R-VALUE / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
RfactorNum. reflection% reflection
Rfree0.268 --
Rwork0.219 --
obs-57748 99.45 %
Refinement stepCycle: LAST / Resolution: 2.8→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8463 0 0 106 8569

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