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- PDB-1bbp: MOLECULAR STRUCTURE OF THE BILIN BINDING PROTEIN (BBP) FROM PIERI... -

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Basic information

Entry
Database: PDB / ID: 1bbp
TitleMOLECULAR STRUCTURE OF THE BILIN BINDING PROTEIN (BBP) FROM PIERIS BRASSICAE AFTER REFINEMENT AT 2.0 ANGSTROMS RESOLUTION.
ComponentsBILIN BINDING PROTEIN
KeywordsBILIN BINDING
Function / homology
Function and homology information


pigment binding / response to reactive oxygen species / lipid metabolic process / extracellular region / cytoplasm
Similarity search - Function
Invertebrate colouration protein / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BILIVERDIN IX GAMMA CHROMOPHORE / Bilin-binding protein
Similarity search - Component
Biological speciesPieris brassicae (large cabbage white)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHuber, R. / Schneider, M. / Mayr, I. / Mueller, R. / Deutzmann, R. / Suter, F. / Zuber, H. / Falk, H. / Kayser, H.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Molecular structure of the bilin binding protein (BBP) from Pieris brassicae after refinement at 2.0 A resolution.
Authors: Huber, R. / Schneider, M. / Mayr, I. / Muller, R. / Deutzmann, R. / Suter, F. / Zuber, H. / Falk, H. / Kayser, H.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Crystallization, Crystal Structure Analysis and Preliminary Molecular Model of the Bilin Binding Protein from the Insect Pieris Brassicae
Authors: Huber, R. / Schneider, M. / Epp, O. / Mayr, I. / Messerschmidt, A. / Pflugrath, J. / Kayser, H.
History
DepositionSep 19, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BILIN BINDING PROTEIN
B: BILIN BINDING PROTEIN
C: BILIN BINDING PROTEIN
D: BILIN BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1438
Polymers78,8124
Non-polymers2,3314
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-90 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.100, 121.900, 63.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9034, 0.1223, 0.411), (-0.1472, -0.9887, -0.0293), (0.4027, -0.087, 0.9112)41.58, 73.07, 4.48
2given(0.2901, 0.9214, -0.2584), (0.9189, -0.3437, -0.1938), (-0.2674, -0.1813, -0.9464)4.44, 23.87, 107.47
3given(-0.2702, -0.9447, -0.1861), (-0.9463, 0.2249, 0.2321), (-0.1774, 0.2388, -0.9547)84.91, 46.31, 101.68
4given(-0.2553, -0.9462, -0.1988), (-0.9519, 0.2099, 0.2233), (-0.1695, 0.2463, -0.9543)85.07, 47.11, 100.8
5given(0.0518, 0.9792, -0.1962), (0.9778, -0.0897, -0.1893), (-0.203, -0.182, -0.9621)12.09, 13.05, 127.72
6given(-0.9008, 0.1123, 0.4194), (-0.127, -0.9919, -0.0072), (0.4152, -0.0598, 0.9078)41.15, 71.32, 3.71
DetailsTHE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW RELATE CHAINS A, B, C, AND D AS FOLLOWS: MTRIX 1: A TO B MTRIX 2: A TO C MTRIX 3: A TO D MTRIX 4: B TO C MTRIX 5: B TO D MTRIX 6: C TO D

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Components

#1: Protein
BILIN BINDING PROTEIN


Mass: 19703.029 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pieris brassicae (large cabbage white) / References: UniProt: P09464
#2: Chemical
ChemComp-BLV / BILIVERDIN IX GAMMA CHROMOPHORE


Mass: 582.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Details: referred to 'Huber, R.', (1987) J.Mol.Biol., 195, 423-434
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein/water1drop
22.8 Mammonium sulfate1drop
30.1 Mimidazole1drop
42.8 Mammonium sulfate1reservoir
50.1 Mimidazole1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.2 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 172 424 6169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.67
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection obs: 51824 / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21 Å2
Refine LS restraints
*PLUS
Type: o_angle_d

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