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- PDB-6vid: The Crystal Structure of Aps Domain-Swapped Trimer Q108K:K40D:T53... -

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Basic information

Entry
Database: PDB / ID: 6vid
TitleThe Crystal Structure of Aps Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Variant of HCRBPII
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / Domain Swapped Trimer / iLBP
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
ACETATE ION / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)R01GM101353 United States
CitationJournal: To Be Published
Title: The Crystal Structure of Apo Domain Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F variant of HCRBPII
Authors: Ghanbarpour, A. / Geiger, J.
History
DepositionJan 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Retinol-binding protein 2
D: Retinol-binding protein 2
E: Retinol-binding protein 2
F: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,98715
Polymers93,2916
Non-polymers6979
Water28816
1
A: Retinol-binding protein 2
B: Retinol-binding protein 2
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,28311
Polymers46,6453
Non-polymers6388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14020 Å2
ΔGint-81 kcal/mol
Surface area18950 Å2
MethodPISA
2
C: Retinol-binding protein 2
E: Retinol-binding protein 2
F: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7044
Polymers46,6453
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-72 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.050, 72.680, 164.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 3 - 132 / Label seq-ID: 3 - 132

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and ((resid 3 and (name N or name...AA
22(chain 'B' and ((resid 3 and (name N or name...BB
33(chain 'C' and (resid 3 through 10 or (resid 11...CC
44(chain 'D' and ((resid 3 and (name N or name...DD
55(chain 'E' and (resid 3 through 25 or (resid 26...EE
66(chain 'F' and (resid 3 through 14 or (resid 15...FF

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Components

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


Mass: 15548.438 Da / Num. of mol.: 6 / Mutation: Q108K, K40D, T53A, R58L, Q38F, Q4F
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: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.07 %
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-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.891→49.282 Å / Num. obs: 18585 / % possible obs: 99.43 % / Redundancy: 7.7 % / Biso Wilson estimate: 61.48 Å2 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.047 / Rrim(I) all: 0.178 / Net I/av σ(I): 22.88 / Net I/σ(I): 2.4
Reflection shellResolution: 2.891→2.994 Å / Rmerge(I) obs: 0.115 / Num. unique obs: 1745 / CC1/2: 0.804 / Rrim(I) all: 1.316

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCQ

2rcq


Resolution: 2.89→49.28 Å / SU ML: 0.3762 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1766 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3078 1852 9.97 %
Rwork0.2454 16726 -
obs0.2515 18578 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.85 Å2
Refinement stepCycle: LAST / Resolution: 2.89→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6105 0 46 16 6167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056258
X-RAY DIFFRACTIONf_angle_d0.91998477
X-RAY DIFFRACTIONf_chiral_restr0.0744950
X-RAY DIFFRACTIONf_plane_restr0.00471091
X-RAY DIFFRACTIONf_dihedral_angle_d7.26323597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.970.37681170.30071182X-RAY DIFFRACTION93.25
2.97-3.060.38091440.30171286X-RAY DIFFRACTION100
3.06-3.160.38621500.29521245X-RAY DIFFRACTION99.93
3.16-3.270.36921520.29061256X-RAY DIFFRACTION100
3.27-3.40.32211260.26561298X-RAY DIFFRACTION99.93
3.4-3.550.33331470.24681277X-RAY DIFFRACTION100
3.55-3.740.31581360.24291275X-RAY DIFFRACTION100
3.74-3.980.28891320.23791291X-RAY DIFFRACTION100
3.98-4.280.29461540.2171287X-RAY DIFFRACTION100
4.28-4.710.26951450.20081297X-RAY DIFFRACTION100
4.71-5.390.26211480.21281289X-RAY DIFFRACTION99.86
5.39-6.790.29221430.25591338X-RAY DIFFRACTION99.93
6.79-49.280.31051580.2621405X-RAY DIFFRACTION99.81

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