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- PDB-4bqu: Japanin from Rhipicephalus appendiculatus bound to cholesterol: O... -

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Basic information

Entry
Database: PDB / ID: 4bqu
TitleJapanin from Rhipicephalus appendiculatus bound to cholesterol: Orthorhombic crystal form
ComponentsJAPANIN
KeywordsCHOLESTEROL-BINDING PROTEIN / TICK
Function / homologyCalycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / extracellular region / Mainly Beta / CHOLESTEROL / Japanin
Function and homology information
Biological speciesRHIPICEPHALUS APPENDICULATUS (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsRoversi, P. / Johnson, S. / Preston, S. / Austyn, J.M. / Nuttall, P. / Lea, S.M.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of cholesterol binding by a novel clade of dendritic cell modulators from ticks.
Authors: Roversi, P. / Johnson, S. / Preston, S.G. / Nunn, M.A. / Paesen, G.C. / Austyn, J.M. / Nuttall, P.A. / Lea, S.M.
History
DepositionJun 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 2.0Dec 13, 2017Group: Atomic model / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JAPANIN
B: JAPANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,28318
Polymers37,2802
Non-polymers3,00316
Water1,38777
1
A: JAPANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2389
Polymers18,6401
Non-polymers1,5988
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: JAPANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0459
Polymers18,6401
Non-polymers1,4058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.180, 133.600, 71.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.951935, -0.085322, -0.294178), (-0.058722, -0.891768, 0.448666), (-0.300619, 0.444376, 0.843894)
Vector: 40.543, -91.978, 28.677)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein JAPANIN


Mass: 18640.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHIPICEPHALUS APPENDICULATUS (arthropod)
Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: M1MR49

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 89 molecules

#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGGHHHHHH AT THE CTERM ARE FROM HIS-TAGGING

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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: 2.57 Å3/Da / Density % sol: 52.1 % / Description: NONE
Crystal growpH: 4.5
Details: 0.2 LITHIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.5 AND 50% V/V PEG 400

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→49.5 Å / Num. obs: 15750 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 48.96 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / % possible all: 81.7

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BOE

4boe


Resolution: 2.36→49.48 Å / Cor.coef. Fo:Fc: 0.9337 / Cor.coef. Fo:Fc free: 0.8936 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.356 / SU Rfree Blow DPI: 0.249
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5430. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5430. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=3.
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 785 5 %RANDOM
Rwork0.196 ---
obs0.1987 15712 97.43 %-
Displacement parametersBiso mean: 56.46 Å2
Baniso -1Baniso -2Baniso -3
1--10.6088 Å20 Å20 Å2
2--9.2519 Å20 Å2
3---1.3569 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.36→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 198 77 2744
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015447HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.149857HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1244SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes725HARMONIC5
X-RAY DIFFRACTIONt_it5447HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion17.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion395SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5798SEMIHARMONIC4
LS refinement shellResolution: 2.36→2.52 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2539 132 5.26 %
Rwork0.2151 2376 -
all0.2171 2508 -
obs--97.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0421-0.05750.5283.4391-1.08972.5606-0.06770.01330.0338-0.27660.10.1484-0.1302-0.0293-0.03230.23820.0014-0.0212-0.1744-0.002-0.235721.0631-31.67839.8121
21.37070.88120.25575.1853-1.01681.8580.0443-0.1033-0.1749-0.15740.0014-0.09960.3325-0.0622-0.04570.13440.0034-0.0338-0.1722-0.0038-0.213420.2106-60.433617.2097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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