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- PDB-2c1s: X-ray structure of biotin binding protein from chicken -

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Basic information

Entry
Database: PDB / ID: 2c1s
TitleX-ray structure of biotin binding protein from chicken
ComponentsBIOTIN BINDING PROTEIN A
KeywordsBIOTIN BINDING PROTEIN
Function / homologyAvidin-like / Lipocalin / Beta Barrel / Mainly Beta / BIOTIN-D-SULFOXIDE
Function and homology information
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHytonen, V.P. / Niskanen, E.A. / Maatta, J.A.E. / Huuskonen, J. / Helttunen, K.J. / Halling, K.K. / Slotte, J.P. / Nordlund, H.R. / Rissanen, K. / Johnson, M.S. ...Hytonen, V.P. / Niskanen, E.A. / Maatta, J.A.E. / Huuskonen, J. / Helttunen, K.J. / Halling, K.K. / Slotte, J.P. / Nordlund, H.R. / Rissanen, K. / Johnson, M.S. / Salminen, T.A. / Kulomaa, M.S. / Laitinen, O.H. / Airenne, T.T.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Structure and Characterization of a Novel Chicken Biotin-Binding Protein a (Bbp-A).
Authors: Hytonen, V.P. / Maatta, J.A.E. / Niskanen, E.A. / Huuskonen, J. / Helttunen, K.J. / Halling, K.K. / Nordlund, H.R. / Rissanen, K. / Johnson, M.S. / Salminen, T.A. / Kulomaa, M.S. / Laitinen, O.H. / Airenne, T.T.
History
DepositionSep 19, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIOTIN BINDING PROTEIN A
B: BIOTIN BINDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5604
Polymers28,0402
Non-polymers5212
Water3,819212
1
A: BIOTIN BINDING PROTEIN A
B: BIOTIN BINDING PROTEIN A
hetero molecules

A: BIOTIN BINDING PROTEIN A
B: BIOTIN BINDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1218
Polymers56,0804
Non-polymers1,0414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.652, 56.049, 57.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2044-

HOH

21B-2047-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.30977, 0.95081, 0.00133), (0.9508, 0.30977, 0.00466), (0.00402, 0.00271, -0.99999)
Vector: 52.17348, -37.88497, 12.22744)

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Components

#1: Protein BIOTIN BINDING PROTEIN A


Mass: 14019.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical ChemComp-BSO / BIOTIN-D-SULFOXIDE / 5-[(3AR,4R,6AS)-5-OXIDO-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID / Biotin sulfoxide


Mass: 260.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.06 Å3/Da / Density % sol: 39.82 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.063
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.063 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 26447 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 13
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WBI

1wbi


Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.731 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1342 5.1 %RANDOM
Rwork0.193 ---
obs0.195 25104 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--1.25 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 34 212 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222043
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9492773
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90723.62691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39715353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6321517
X-RAY DIFFRACTIONr_chiral_restr0.1130.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021515
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2909
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21399
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.2123
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0111.51259
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67621995
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3563902
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5594.5778
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 113
Rwork0.26 1802

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