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- PDB-7ucz: The Crystal Structure of Apo Monomer F57:H:H:H:H:H:H:R58 Mutant o... -

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Basic information

Entry
Database: PDB / ID: 7ucz
TitleThe Crystal Structure of Apo Monomer F57:H:H:H:H:H:H:R58 Mutant of HCRBPII with Histidine Insertion in the Hinge Loop Region at 1.1 Angstrom Resolution
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / LBP / CRBPII
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / Retinoid metabolism and transport / fatty acid 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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: The Crystal Structure of Domain-Sawpped Dimer Q108K:T51D:A28C:L36C:F57:H:R58 Mutant of hCRBPII with a Histidine Insertion in the Hinge Loop Region at 1.96 Angstrom Resolution
Authors: Ghanbarpour, A. / Geiger, J.
History
DepositionMar 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)32,8532
Polymers32,8532
Non-polymers00
Water4,756264
1
A: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)16,4261
Polymers16,4261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)16,4261
Polymers16,4261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.608, 36.931, 68.513
Angle α, β, γ (deg.)73.414, 83.918, 66.059
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 16426.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2
Production host: Bacterial expression vector pBEN1-SGC (others)
References: UniProt: P50120
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, sodium acetate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.079→27.06 Å / Num. obs: 101925 / % possible obs: 93.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.079 / Net I/av σ(I): 33.3 / Net I/σ(I): 33.3
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 9597 / Rrim(I) all: 0.593 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCQ

2rcq


Resolution: 1.08→27.06 Å / SU ML: 0.0941 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 22.5672 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 2003 1.97 %
Rwork0.2 99913 -
obs0.2002 101916 93.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.94 Å2
Refinement stepCycle: LAST / Resolution: 1.08→27.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 0 264 2554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432385
X-RAY DIFFRACTIONf_angle_d0.74353226
X-RAY DIFFRACTIONf_chiral_restr0.0834344
X-RAY DIFFRACTIONf_plane_restr0.0038417
X-RAY DIFFRACTIONf_dihedral_angle_d21.2475884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.110.23431280.25566584X-RAY DIFFRACTION85.47
1.11-1.140.2771400.24186903X-RAY DIFFRACTION89.95
1.14-1.170.25591330.23346854X-RAY DIFFRACTION90.31
1.17-1.210.221440.22646973X-RAY DIFFRACTION91.13
1.21-1.250.23731380.2267071X-RAY DIFFRACTION91.64
1.25-1.30.22691450.22647070X-RAY DIFFRACTION92.39
1.3-1.360.21551480.21657157X-RAY DIFFRACTION92.83
1.36-1.430.22841440.21247153X-RAY DIFFRACTION93.66
1.43-1.520.26751500.20467181X-RAY DIFFRACTION94.25
1.52-1.640.18781480.18967313X-RAY DIFFRACTION95.02
1.64-1.80.21541450.20027312X-RAY DIFFRACTION95.73
1.8-2.060.22021480.19417419X-RAY DIFFRACTION96.48
2.06-2.60.24571420.19767442X-RAY DIFFRACTION97.23
2.6-27.060.17591500.18577481X-RAY DIFFRACTION97.5
Refinement TLS params.Method: refined / Origin x: 1.8636865831 Å / Origin y: 24.8288324346 Å / Origin z: 6.80792523658 Å
111213212223313233
T0.0779403373618 Å2-0.00294233212924 Å2-0.00225519142645 Å2-0.0891021647045 Å20.00816997399539 Å2--0.101811250821 Å2
L0.1393238815 °2-0.00349614546409 °20.0417921040958 °2-0.403051056048 °20.367310765616 °2--0.818217144813 °2
S-0.0032035164294 Å °0.0105364837057 Å °0.00810302529615 Å °0.0146100616295 Å °0.00318630551053 Å °0.00621358868789 Å °-0.0191630576639 Å °0.0188214441035 Å °-0.00512567896817 Å °
Refinement TLS groupSelection details: all

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