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- PDB-4ruu: Crystal structure of the Q108K:K40L mutant of human Cellular Reti... -

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Basic information

Entry
Database: PDB / ID: 4ruu
TitleCrystal structure of the Q108K:K40L mutant of human Cellular Retinol Binding ProteinII in complex with All-trans-Retinal after 24 hour incubation at 1.4 Angstrom Resolution
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / Wavelength regulation
Function / homology
Function and homology information


vitamin A metabolic process / molecular carrier activity / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNosrati, M. / Geiger, J.H.
CitationJournal: Science / Year: 2012
Title: Tuning the electronic absorption of protein-embedded all-trans-retinal.
Authors: Wang, W. / Nossoni, Z. / Berbasova, T. / Watson, C.T. / Yapici, I. / Lee, K.S. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...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 / 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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: Retinol-binding protein 2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8526
Polymers31,1652
Non-polymers6874
Water5,062281
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9263
Polymers15,5821
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9263
Polymers15,5821
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.479, 36.570, 64.093
Angle α, β, γ (deg.)86.54, 86.60, 64.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15582.481 Da / Num. of mol.: 2 / Mutation: K40L, Q108K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: Pet17b / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 30 % PEG 4000, 0.1 M Ammonium Acatate, 0.1 M Sodium Acetate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 47535 / % possible obs: 95 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.09 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 43.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.233 / % possible all: 92.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RCT

2rct


Resolution: 1.4→29.852 Å / SU ML: 0.4 / σ(F): 1.98 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 2288 5.06 %
Rwork0.2074 --
obs0.2089 45174 94.97 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.226 Å2 / ksol: 0.422 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0444 Å20.0044 Å20.1482 Å2
2--0.6283 Å2-0.291 Å2
3----0.5839 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 35 281 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072269
X-RAY DIFFRACTIONf_angle_d1.0963055
X-RAY DIFFRACTIONf_dihedral_angle_d15.315841
X-RAY DIFFRACTIONf_chiral_restr0.077328
X-RAY DIFFRACTIONf_plane_restr0.004397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4003-1.43070.32591500.3052562X-RAY DIFFRACTION92
1.4307-1.4640.30131540.29482651X-RAY DIFFRACTION94
1.464-1.50060.34311420.27092639X-RAY DIFFRACTION94
1.5006-1.54120.30691460.24852688X-RAY DIFFRACTION94
1.5412-1.58650.26931100.24472664X-RAY DIFFRACTION95
1.5865-1.63770.30751500.23082744X-RAY DIFFRACTION96
1.6377-1.69630.28651550.22292647X-RAY DIFFRACTION96
1.6963-1.76420.27361560.21832688X-RAY DIFFRACTION96
1.7642-1.84440.24281540.22292743X-RAY DIFFRACTION96
1.8444-1.94170.26741470.2092718X-RAY DIFFRACTION96
1.9417-2.06330.24921420.19742686X-RAY DIFFRACTION96
2.0633-2.22250.22541340.20432779X-RAY DIFFRACTION97
2.2225-2.44610.22131420.20262773X-RAY DIFFRACTION97
2.4461-2.79990.23131450.20412737X-RAY DIFFRACTION98
2.7999-3.52660.23971430.18932750X-RAY DIFFRACTION98
3.5266-29.85860.19481180.20032417X-RAY DIFFRACTION85
Refinement TLS params.Method: refined / Origin x: -1.1998 Å / Origin y: 0.4353 Å / Origin z: 15.2603 Å
111213212223313233
T0.1232 Å20.0168 Å2-0.0043 Å2-0.1297 Å20.0016 Å2--0.1654 Å2
L0.0995 °20.1585 °2-0.1768 °2-0.0008 °20.3231 °2--3.9394 °2
S-0.0102 Å °0.0055 Å °-0.0333 Å °0.0118 Å °-0.0365 Å °-0.0011 Å °-0.0019 Å °-0.0805 Å °0.0471 Å °
Refinement TLS groupSelection details: all

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