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- PDB-7ucs: The Crystal Structure of Domain-Swapped Dimer Q108K:T51D:A28C:L36... -

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Basic information

Entry
Database: PDB / ID: 7ucs
TitleThe Crystal Structure of Domain-Swapped Dimer Q108K:T51D:A28C:L36C:F57:H:H:H:R58 Mutant of hCRBPII with Histidine Insertion in the Hinge Loop Region at 1.92 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: 1.92 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)32,0982
Polymers32,0982
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-41 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.929, 69.982, 106.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain 'A' and (resid 1 through 26 or (resid 27...AA1 - 531 - 53
12SERSERCYSCYS(chain 'A' and (resid 1 through 26 or (resid 27...AA55 - 9855 - 98
13GLNGLNLYSLYS(chain 'A' and (resid 1 through 26 or (resid 27...AA100 - 101100 - 101
14LYSLYSASPASP(chain 'A' and (resid 1 through 26 or (resid 27...AA104 - 116104 - 116
15LEULEULYSLYS(chain 'A' and (resid 1 through 26 or (resid 27...AA118 - 136118 - 136
21THRTHRTHRTHR(chain 'B' and (resid 1 through 49 or (resid 50...BB1 - 531 - 53
22SERSERCYSCYS(chain 'B' and (resid 1 through 49 or (resid 50...BB55 - 9855 - 98
23GLNGLNLYSLYS(chain 'B' and (resid 1 through 49 or (resid 50...BB100 - 101100 - 101
24LYSLYSASPASP(chain 'B' and (resid 1 through 49 or (resid 50...BB104 - 116104 - 116
25LEULEULYSLYS(chain 'B' and (resid 1 through 49 or (resid 50...BB118 - 136118 - 136

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Components

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


Mass: 16048.981 Da / Num. of mol.: 2 / Mutation: A28C, L36C, T51D, Q111K
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.: 49 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate, PEG4000, 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: 0.97626 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.92→34.89 Å / Num. obs: 21404 / % possible obs: 98.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 24.82 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.7
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2032 / % possible all: 99.8

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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: 1.92→34.89 Å / SU ML: 0.1998 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.5847 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 2000 9.34 %
Rwork0.1954 19404 -
obs0.1986 21404 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.84 Å2
Refinement stepCycle: LAST / Resolution: 1.92→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 0 49 2283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692307
X-RAY DIFFRACTIONf_angle_d0.84223114
X-RAY DIFFRACTIONf_chiral_restr0.0564332
X-RAY DIFFRACTIONf_plane_restr0.005402
X-RAY DIFFRACTIONf_dihedral_angle_d17.07331380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.28091330.21241291X-RAY DIFFRACTION93.68
1.97-2.020.27831420.19791374X-RAY DIFFRACTION100
2.02-2.080.26971430.20241386X-RAY DIFFRACTION99.74
2.08-2.150.25511410.21021368X-RAY DIFFRACTION99.8
2.15-2.230.28341410.19731377X-RAY DIFFRACTION99.74
2.23-2.320.24571470.2121416X-RAY DIFFRACTION99.49
2.32-2.420.28131400.20591363X-RAY DIFFRACTION99.87
2.42-2.550.25561440.20831400X-RAY DIFFRACTION99.87
2.55-2.710.24281430.21861387X-RAY DIFFRACTION99.67
2.71-2.920.20641440.2121395X-RAY DIFFRACTION99.55
2.92-3.210.24421450.20981406X-RAY DIFFRACTION99.36
3.21-3.670.22031450.1831412X-RAY DIFFRACTION98.11
3.67-4.630.19231420.16841367X-RAY DIFFRACTION94.61
4.63-34.890.19761500.18781462X-RAY DIFFRACTION96.07
Refinement TLS params.Method: refined / Origin x: -8.77363254301 Å / Origin y: -8.42833121013 Å / Origin z: 119.277070102 Å
111213212223313233
T0.213186334028 Å2-0.00451924598091 Å20.019387350271 Å2-0.192264289104 Å20.0249244988841 Å2--0.193810393592 Å2
L1.28290924918 °20.793599145239 °2-0.289523375473 °2-0.580674587484 °2-0.273153517987 °2--0.19294898747 °2
S-0.0921348842376 Å °0.110312638387 Å °-0.0278117406334 Å °-0.122797742641 Å °0.0559317977449 Å °-0.0346462118872 Å °0.0784543705927 Å °-0.0370250767769 Å °0.0403415077942 Å °
Refinement TLS groupSelection details: all

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