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- PDB-3hx3: Crystal structure of CRALBP mutant R234W -

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Basic information

Entry
Database: PDB / ID: 3hx3
TitleCrystal structure of CRALBP mutant R234W
ComponentsRetinaldehyde-binding protein 1
KeywordsTRANSPORT PROTEIN / lipid transfer protein / 11-cis-retinal / bothnia dystrophy / Acetylation / Cytoplasm / Disease mutation / Retinitis pigmentosa / Retinol-binding / Sensory transduction / Transport / Vision
Function / homology
Function and homology information


The retinoid cycle in cones (daylight vision) / 11-cis retinal binding / vitamin A metabolic process / retinol binding / phosphatidylinositol bisphosphate binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / visual perception / cell body / centrosome ...The retinoid cycle in cones (daylight vision) / 11-cis retinal binding / vitamin A metabolic process / retinol binding / phosphatidylinositol bisphosphate binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / visual perception / cell body / centrosome / nucleoplasm / cytosol
Similarity search - Function
N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) ...N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RETINAL / Retinaldehyde-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsStocker, A. / He, X. / Lobsiger, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Bothnia dystrophy is caused by domino-like rearrangements in cellular retinaldehyde-binding protein mutant R234W.
Authors: He, X. / Lobsiger, J. / Stocker, A.
History
DepositionJun 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinaldehyde-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9782
Polymers36,6931
Non-polymers2841
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.930, 57.880, 75.150
Angle α, β, γ (deg.)90.000, 122.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-679-

HOH

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Components

#1: Protein Retinaldehyde-binding protein 1 / Cellular retinaldehyde-binding protein


Mass: 36693.340 Da / Num. of mol.: 1 / Mutation: R234W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRALBP, RLBP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12271
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG 3000, NaCl, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2008
RadiationMonochromator: Si(111) Channel / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.69→45.577 Å / Num. all: 69614 / Num. obs: 67824 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 30.96 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.8
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.7 / Num. unique all: 11226 / Num. unique obs: 9663 / % possible all: 86.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.78 Å / D res low: 19.45 Å / FOM : 0.53 / FOM acentric: 0.547 / FOM centric: 0.169 / Reflection: 30506 / Reflection acentric: 29134 / Reflection centric: 1362
Phasing dmFOM : 0.69 / FOM acentric: 0.7 / FOM centric: 0.52 / Reflection: 30515 / Reflection acentric: 29153 / Reflection centric: 1362
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.1-19.4510.940.950.8513421187155
3.2-5.10.930.950.7340923833259
2.5-3.20.840.850.5951134867246
2.2-2.50.750.760.4451394930209
1.9-2.20.580.590.3291578840317
1.8-1.90.440.440.2856725496176

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.69→45.577 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 0 / Stereochemistry target values: ML
Details: The Friedel pairs were used in phasing and in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 6775 9.99 %RANDOM
Rwork0.167 ---
all0.169 67814 --
obs0.169 67814 97.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.973 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 110.75 Å2 / Biso mean: 32.6 Å2 / Biso min: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1-8.166 Å20 Å21.778 Å2
2---3.148 Å2-0 Å2
3----5.018 Å2
Refine analyzeLuzzati coordinate error obs: 0.2039 Å
Refinement stepCycle: LAST / Resolution: 1.69→45.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 21 383 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052115
X-RAY DIFFRACTIONf_angle_d1.1762855
X-RAY DIFFRACTIONf_chiral_restr0.165301
X-RAY DIFFRACTIONf_plane_restr0.004375
X-RAY DIFFRACTIONf_dihedral_angle_d16.824773
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.7120.3541030.336939104245
1.712-1.7320.2932040.2641821202588
1.732-1.7530.2782360.24621312367100
1.753-1.7750.242210.22720002221100
1.775-1.7980.2522340.2121092343100
1.798-1.8230.2032330.18521172350100
1.823-1.8490.2222240.1820232247100
1.849-1.8770.212400.18421832423100
1.877-1.9060.2142230.18319832206100
1.906-1.9370.2072390.16921182357100
1.937-1.9710.1992250.16720482273100
1.971-2.0070.1952330.17120862319100
2.007-2.0450.1782350.16221052340100
2.045-2.0870.1812290.16220452274100
2.087-2.1320.182350.16120962331100
2.132-2.1820.192300.15620882318100
2.182-2.2370.1792290.16420722301100
2.237-2.2970.1772330.16320832316100
2.297-2.3650.1882300.15520722302100
2.365-2.4410.1772350.16720842319100
2.441-2.5280.1952300.15520742304100
2.528-2.6290.2142320.16921332365100
2.629-2.7490.1832260.17120782304100
2.749-2.8940.1772320.17420792311100
2.894-3.0750.1772270.17220592286100
3.075-3.3130.1652370.1621002337100
3.313-3.6460.162330.1520892322100
3.646-4.1730.1542290.14320642293100
4.173-5.2560.1592300.13921012331100
5.256-45.5770.1632280.1742059228799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.60190.48180.4186-0.3050.16754.4604-0.16310.00660.4085-0.1645-0.05560.2029-0.974-0.27370.23020.32030.1716-0.08410.1459-0.03390.2933-14.247531.98989.0131
2-0.0307-1.4097-1.16312.81010.91481.95590.00180.2903-0.48570.1249-0.12290.706-0.1689-0.34670.13840.09150.0990.01650.1851-0.06190.2869-17.087923.549113.8514
3-0.3663-0.30890.40310.8804-0.03971.357-0.0161-0.0367-0.00650.0154-0.0360.2672-0.0855-0.24630.01340.03140.01160.03210.10690.00630.1078-9.733916.36712.8236
40.98040.43960.58811.70950.05031.35670.0864-0.0443-0.17160.40.02950.0470.1934-0.0592-0.10940.1075-0.0150.01340.04070.01780.077-3.32164.740620.545
50.3725-0.04760.54571.0938-0.3040.61190.01640.12490.02110.1296-0.0285-0.089-0.02470.14340.01090.04020.01210.00280.08230.00460.07213.3587.3915.0643
60.64590.0970.64611.3420.37090.20420.01730.05750.00630.41040.0021-0.1442-0.01740.12510.00550.1218-0.0136-0.04690.05130.01310.08799.1968.06124.3765
70.03030.33851.0908-0.80370.3452-0.41330.3929-0.4911-0.0240.2935-0.02250.1425-0.2543-0.2914-0.35490.2483-0.01290.12660.24750.13560.1667-11.2113.228229.1944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 57:85)A57 - 85
2X-RAY DIFFRACTION2(chain A and resid 86:98)A86 - 98
3X-RAY DIFFRACTION3(chain A and resid 99:143)A99 - 143
4X-RAY DIFFRACTION4(chain A and resid 144:185)A144 - 185
5X-RAY DIFFRACTION5(chain A and resid 186:255)A186 - 255
6X-RAY DIFFRACTION6(chain A and resid 256:295)A256 - 295
7X-RAY DIFFRACTION7(chain A and resid 296:306)A296 - 306

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