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- PDB-7ud1: The Crystal Structure of Apo Monomer F57:H:H:H:R58 HCRBPII with H... -

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Basic information

Entry
Database: PDB / ID: 7ud1
TitleThe Crystal Structure of Apo Monomer F57:H:H:H:R58 HCRBPII with Histidine Insertion in the Hinge Loop Region at 1.3 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 / 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
Similarity search - Domain/homology
Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 Apo Monomer F57:H:H:H:R58 HCRBPII with Histidine Insertion in the Hinge Loop Region at 1.3 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)32,0242
Polymers32,0242
Non-polymers00
Water6,107339
1
A: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)16,0121
Polymers16,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)16,0121
Polymers16,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.525, 47.815, 53.223
Angle α, β, γ (deg.)90.000, 92.615, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 16011.896 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 / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 298 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-D / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.32→29.09 Å / Num. obs: 55379 / % possible obs: 96.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.087 / Net I/σ(I): 27.9
Reflection shellResolution: 1.964→2.035 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 5345 / Rrim(I) all: 0.602 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCQ

2rcq


Resolution: 1.32→29.09 Å / SU ML: 0.1369 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2125 2009 3.63 %
Rwork0.1866 53370 -
obs0.1876 55379 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.73 Å2
Refinement stepCycle: LAST / Resolution: 1.32→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 0 339 2589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532298
X-RAY DIFFRACTIONf_angle_d0.80173095
X-RAY DIFFRACTIONf_chiral_restr0.0895329
X-RAY DIFFRACTIONf_plane_restr0.0071399
X-RAY DIFFRACTIONf_dihedral_angle_d5.993294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.350.25671330.25193635X-RAY DIFFRACTION91.63
1.35-1.390.28221420.23783713X-RAY DIFFRACTION94.55
1.39-1.430.27581300.22413649X-RAY DIFFRACTION92.94
1.43-1.480.24711350.20363697X-RAY DIFFRACTION94.01
1.48-1.530.1921500.19193878X-RAY DIFFRACTION98.75
1.53-1.590.2181520.18823885X-RAY DIFFRACTION99.02
1.59-1.660.21771520.18153882X-RAY DIFFRACTION98.27
1.66-1.750.23611420.18343876X-RAY DIFFRACTION98.6
1.75-1.860.20181410.18813850X-RAY DIFFRACTION97.89
1.86-20.22051390.1793886X-RAY DIFFRACTION98.08
2-2.20.17121520.17873825X-RAY DIFFRACTION96.86
2.2-2.520.19521420.18063640X-RAY DIFFRACTION91.66
2.52-3.180.22721470.19333941X-RAY DIFFRACTION99.22
3.18-29.090.20821520.17634013X-RAY DIFFRACTION98.81
Refinement TLS params.Method: refined / Origin x: 60.0223476086 Å / Origin y: -20.5987725934 Å / Origin z: 13.7485355522 Å
111213212223313233
T0.0928346754422 Å2-0.00563208114726 Å20.000468689497538 Å2-0.0879654451474 Å2-0.00505793444003 Å2--0.0963321211167 Å2
L0.127807829534 °2-0.0184410256678 °2-0.0225880463436 °2-0.094144479117 °20.222287814417 °2--0.497494369354 °2
S0.0274720394872 Å °0.0083850123413 Å °0.00654590738282 Å °0.00456597534063 Å °-0.00797395987155 Å °0.00369482892816 Å °-0.0158088320186 Å °0.0257925468076 Å °0.00876578597191 Å °
Refinement TLS groupSelection details: all

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