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- PDB-4lur: Crystal Structure of Zebrafish Interphotoreceptor Retinoid-Bindin... -

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Basic information

Entry
Database: PDB / ID: 4lur
TitleCrystal Structure of Zebrafish Interphotoreceptor Retinoid-Binding Protein (IRBP) Module 1
ComponentsInterphotoreceptor Retinoid-Binding Protein(IRBP)
KeywordsTRANSPORT PROTEIN / Multi-module structure / proteases activity
Function / homology
Function and homology information


all-trans-retinol binding / oleic acid binding / serine-type peptidase activity / proteolysis
Similarity search - Function
N-terminal domain of Peptidase_S41 in eukaryotic IRBP / tail specific protease / Tail specific protease / Peptidase family S41 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
OLEIC ACID / Retinol-binding protein 3
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD COMBINED WITH MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGhosh, D. / Gonzalez-Fernandez, F.
CitationJournal: To be Published
Title: Structure of Zebrafish IRBP Reveals Its Fatty Acid Binding Sites and Retention of Protease Fold
Authors: Ghosh, D. / Haswell, K.M. / Sprada, M. / Gonzalez-Fernandez, F.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interphotoreceptor Retinoid-Binding Protein(IRBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7006
Polymers33,9021
Non-polymers7975
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.295, 97.771, 41.214
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 Interphotoreceptor Retinoid-Binding Protein(IRBP)


Mass: 33902.473 Da / Num. of mol.: 1 / Fragment: UNP residues 22-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Escherichia coli (E. coli) / References: UniProt: F1Q9N9
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 295 K / pH: 7.5
Details: Protein solutions at a concentration of 20mg/ml were mixed with the reservoir solutions of 35-44% polyethylene glycol 8000 in 100mM HEPES pH 7.5 buffer containing 100mM NaBr in the 1:1, 2:1 ...Details: Protein solutions at a concentration of 20mg/ml were mixed with the reservoir solutions of 35-44% polyethylene glycol 8000 in 100mM HEPES pH 7.5 buffer containing 100mM NaBr in the 1:1, 2:1 and 3:1 volume ratios and vapor diffused against the reservoir solutions. Plate-shaped crystals appeared in about a week and continued to grow for a few more weeks., VAPOR DIFFUSION, SITTING DROP, temperature 295.K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979368, 0.979484, 0.9716932
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2009
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9793681
20.9794841
30.97169321
ReflectionResolution: 1.9→50 Å / Num. obs: 27277 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 40
Reflection shellResolution: 1.901→1.95 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MAD COMBINED WITH MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J7X

1j7x


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.273 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1332 5 %RANDOM
Rwork0.219 ---
obs0.222 25467 98.3 %-
all-27277 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20 Å2
2--2.41 Å2-0 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 53 165 2556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222425
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3742.0133293
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26225.82379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5815418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.23156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211717
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_it0.7921.51545
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53422517
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.513880
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0084.5776
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 100 -
Rwork0.297 1786 -
obs--95.01 %

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