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- PDB-7ud3: The Crystal Structure of Domain-Swapped Dimer Q108K:T51D:A28C:L36... -

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Basic information

Entry
Database: PDB / ID: 7ud3
TitleThe Crystal Structure of Domain-Swapped Dimer Q108K:T51D:A28C:L36C:F57:W:W:W:R58 Mutant of hCRBPII with a Histidine Insertion in the Hinge Loop Region at 2.36 Angstrom Resolution
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / LBP / CRBPII
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
Similarity search - Domain/homology
Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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
Revision 1.1Oct 16, 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
C: Retinol-binding protein 2
D: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)64,7734
Polymers64,7734
Non-polymers00
Water63135
1
A: Retinol-binding protein 2
B: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)32,3862
Polymers32,3862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-39 kcal/mol
Surface area14250 Å2
MethodPISA
2
C: Retinol-binding protein 2
D: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)32,3862
Polymers32,3862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-40 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.652, 140.652, 63.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

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
11THRTHRILEILE(chain 'A' and (resid 1 through 33 or resid 35...AA1 - 321 - 32
12ARGARGTHRTHR(chain 'A' and (resid 1 through 33 or resid 35...AA35 - 5435 - 54
13THRTHRARGARG(chain 'A' and (resid 1 through 33 or resid 35...AA56 - 8356 - 83
14VALVALCYSCYS(chain 'A' and (resid 1 through 33 or resid 35...AA85 - 9885 - 98
15GLNGLNLYSLYS(chain 'A' and (resid 1 through 33 or resid 35...AA100 - 136100 - 136
21THRTHRILEILE(chain 'B' and (resid 1 through 33 or resid 35...BB1 - 321 - 32
22ARGARGTHRTHR(chain 'B' and (resid 1 through 33 or resid 35...BB35 - 5435 - 54
23THRTHRARGARG(chain 'B' and (resid 1 through 33 or resid 35...BB56 - 8356 - 83
24VALVALCYSCYS(chain 'B' and (resid 1 through 33 or resid 35...BB85 - 9885 - 98
25GLNGLNLYSLYS(chain 'B' and (resid 1 through 33 or resid 35...BB100 - 136100 - 136
31THRTHRILEILE(chain 'C' and (resid 1 through 33 or resid 35...CC1 - 321 - 32
32ARGARGTHRTHR(chain 'C' and (resid 1 through 33 or resid 35...CC35 - 5435 - 54
33THRTHRARGARG(chain 'C' and (resid 1 through 33 or resid 35...CC56 - 8356 - 83
34VALVALCYSCYS(chain 'C' and (resid 1 through 33 or resid 35...CC85 - 9885 - 98
35GLNGLNLYSLYS(chain 'C' and (resid 1 through 33 or resid 35...CC100 - 136100 - 136
41THRTHRILEILE(chain 'D' and (resid 1 through 33 or resid 35...DD1 - 321 - 32
42ARGARGTHRTHR(chain 'D' and (resid 1 through 33 or resid 35...DD35 - 5435 - 54
43THRTHRARGARG(chain 'D' and (resid 1 through 33 or resid 35...DD56 - 8356 - 83
44VALVALCYSCYS(chain 'D' and (resid 1 through 33 or resid 35...DD85 - 9885 - 98
45GLNGLNLYSLYS(chain 'D' and (resid 1 through 33 or resid 35...DD100 - 136100 - 136

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Components

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


Mass: 16193.169 Da / Num. of mol.: 4 / 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 pAIL2 (others) / References: UniProt: P50120
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 4000 PEG, 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 MX-300 / Detector: CCD / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.369→44.85 Å / Num. obs: 25561 / % possible obs: 99.83 % / Redundancy: 7.3 % / Biso Wilson estimate: 46.87 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 30.19
Reflection shellResolution: 2.369→2.454 Å / Redundancy: 7 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.81 / Num. unique obs: 2499 / % possible all: 98.85

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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: 2.37→44.85 Å / SU ML: 0.3436 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8337 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 2004 7.84 %
Rwork0.1871 23554 -
obs0.1927 25558 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.94 Å2
Refinement stepCycle: LAST / Resolution: 2.37→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 0 35 4574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814662
X-RAY DIFFRACTIONf_angle_d0.9456291
X-RAY DIFFRACTIONf_chiral_restr0.0593654
X-RAY DIFFRACTIONf_plane_restr0.0059800
X-RAY DIFFRACTIONf_dihedral_angle_d19.55422741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.36371420.2561638X-RAY DIFFRACTION98.4
2.43-2.490.35151440.23781667X-RAY DIFFRACTION100
2.49-2.570.34841400.24591666X-RAY DIFFRACTION100
2.57-2.650.29591450.23121697X-RAY DIFFRACTION100
2.65-2.750.32161430.21911655X-RAY DIFFRACTION100
2.75-2.850.26151400.22711671X-RAY DIFFRACTION100
2.85-2.980.32911450.23531683X-RAY DIFFRACTION100
2.98-3.140.33971410.23271684X-RAY DIFFRACTION100
3.14-3.340.2851460.22691663X-RAY DIFFRACTION100
3.34-3.60.30511400.19511698X-RAY DIFFRACTION100
3.6-3.960.241440.1731684X-RAY DIFFRACTION100
3.96-4.530.21861430.14741700X-RAY DIFFRACTION100
4.53-5.710.19141420.14741703X-RAY DIFFRACTION99.95
5.71-44.850.21241490.16371745X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: -30.0206912129 Å / Origin y: -18.43699304 Å / Origin z: -16.0674640193 Å
111213212223313233
T0.325683157623 Å2-0.0248485103124 Å20.0112010475039 Å2-0.370744201493 Å20.00217483360904 Å2--0.354403117397 Å2
L0.121342804612 °20.0333875150807 °20.148229684389 °2-0.58843974051 °2-0.0908581558004 °2--0.340964527276 °2
S-0.00578276716254 Å °0.0581378524454 Å °0.0184756105136 Å °0.119878310964 Å °-0.0314517408488 Å °0.0720141007371 Å °-0.0695499984351 Å °0.0507810056734 Å °0.0364225973369 Å °
Refinement TLS groupSelection details: all

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