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- PDB-1avd: THREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG... -

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Basic information

Entry
Database: PDB / ID: 1avd
TitleTHREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG-WHITE AVIDIN IN ITS FUNCTIONAL COMPLEX WITH BIOTIN AT 2.7 ANGSTROMS RESOLUTION
ComponentsAVIDIN
KeywordsBIOTIN-BINDING PROTEIN
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsPugliese, L. / Coda, A. / Malcovati, M. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution.
Authors: Pugliese, L. / Coda, A. / Malcovati, M. / Bolognesi, M.
#1: Journal: To be Published
Title: Crystal Structure of Hen Egg-White Apo-Avidin in Relation to its Thermal Stability Properties
Authors: Pugliese, L. / Malcovati, M. / Coda, A. / Bolognesi, M.
#2: Journal: J.Mol.Biol. / Year: 1984
Title: Crystallization of Hen Egg-White Avidin in a Tetragonal Form
Authors: Gatti, G. / Bolognesi, M. / Coda, A. / Chiolerio, F. / Filippini, E. / Malcovati, M.
History
DepositionMar 5, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE SHEET PRESENTED AS *CH1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *CH1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-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: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4105
Polymers28,7002
Non-polymers7103
Water66737
1
A: AVIDIN
B: AVIDIN
hetero molecules

A: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,82010
Polymers57,4004
Non-polymers1,4206
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area13400 Å2
ΔGint-30 kcal/mol
Surface area20250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.150, 80.150, 85.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.5282, 0.849, -0.009), (0.849, 0.5282, -0.007), (-0.0012, -0.012, -1)
Vector: 61.4402, -33.8112, 57.6853)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein AVIDIN


Mass: 14350.081 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P02701
#2: 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
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPOSITION 34 SHOWS RESIDUE MICROHETEROGENEITY (THR OR ILE), AS DETERMINED FROM AMINO ACID SEQUENCING. ...POSITION 34 SHOWS RESIDUE MICROHETEROGENEITY (THR OR ILE), AS DETERMINED FROM AMINO ACID SEQUENCING. THE ELECTRON DENSITY HAS BEEN INTERPRETED AS THR, ALTHOUGH THE PRESENCE OF A MINOR ILE COMPONENT IN THE CRYSTAL CANNOT BE EXCLUDED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal grow
*PLUS
pH: 5.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein solution1drop
20.05 Mphosphate1drop
32.0 Mammonium sulfate1drop
42.5 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 8087 / Num. measured all: 69005 / Rmerge(I) obs: 0.129

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.174 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 46 37 2022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.93
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 7255 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 3 Å

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