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- PDB-4jhn: The crystal structure of the RPGR RCC1-like domain -

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Basic information

Entry
Database: PDB / ID: 4jhn
TitleThe crystal structure of the RPGR RCC1-like domain
ComponentsX-linked retinitis pigmentosa GTPase regulator
KeywordsUNKNOWN FUNCTION / RCC1 / beta propellar / seven bladed-propeller
Function / homology
Function and homology information


intraciliary transport / sperm flagellum / cilium assembly / photoreceptor outer segment / visual perception / guanyl-nucleotide exchange factor activity / intracellular protein transport / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination ...intraciliary transport / sperm flagellum / cilium assembly / photoreceptor outer segment / visual perception / guanyl-nucleotide exchange factor activity / intracellular protein transport / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ciliary basal body / centrosome / Golgi apparatus / RNA binding / cytoplasm
Similarity search - Function
: / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Mainly Beta
Similarity search - Domain/homology
X-linked retinitis pigmentosa GTPase regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWaetzlich, D. / Vetter, I. / Wittinghofer, A. / Ismail, S.
CitationJournal: Embo Rep. / Year: 2013
Title: The interplay between RPGR, PDE-delta and Arl2/3 regulate the ciliary targeting of farnesylated cargo.
Authors: Watzlich, D. / Vetter, I. / Gotthardt, K. / Miertzschke, M. / Chen, Y.X. / Wittinghofer, A. / Ismail, S.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: X-linked retinitis pigmentosa GTPase regulator
B: X-linked retinitis pigmentosa GTPase regulator
C: X-linked retinitis pigmentosa GTPase regulator
D: X-linked retinitis pigmentosa GTPase regulator


Theoretical massNumber of molelcules
Total (without water)183,8634
Polymers183,8634
Non-polymers00
Water18,7181039
1
A: X-linked retinitis pigmentosa GTPase regulator


Theoretical massNumber of molelcules
Total (without water)45,9661
Polymers45,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: X-linked retinitis pigmentosa GTPase regulator


Theoretical massNumber of molelcules
Total (without water)45,9661
Polymers45,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: X-linked retinitis pigmentosa GTPase regulator


Theoretical massNumber of molelcules
Total (without water)45,9661
Polymers45,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: X-linked retinitis pigmentosa GTPase regulator


Theoretical massNumber of molelcules
Total (without water)45,9661
Polymers45,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.490, 118.730, 92.630
Angle α, β, γ (deg.)90.00, 101.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
X-linked retinitis pigmentosa GTPase regulator


Mass: 45965.641 Da / Num. of mol.: 4 / Fragment: RPGR (1-392) the RCC1-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPGR, RP3, XLRP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92834
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1039 / 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: 1.68 Å3/Da / Density % sol: 26.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M LiCl2 and 18% (w/v) PEG3350 and microseeding, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2010
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.7→29.83 Å / Num. all: 132539 / Num. obs: 132539 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 5.17 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
REFMAC5.6.0093refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A12

1a12


Resolution: 1.7→29.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.201 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21835 6627 5 %RANDOM
Rwork0.18541 ---
obs0.18703 125911 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.676 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.55 Å2
2--1.4 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 0 1039 11971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211273
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9415300
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96551473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14524.99485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.368151809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3691529
X-RAY DIFFRACTIONr_chiral_restr0.0720.21696
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218606
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 483 -
Rwork0.217 9212 -
obs--99.65 %

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