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- PDB-3mm0: Crystal structure of chimeric avidin -

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Basic information

Entry
Database: PDB / ID: 3mm0
TitleCrystal structure of chimeric avidin
ComponentsAvidin, Avidin-related protein 4/5
KeywordsBIOTIN BINDING PROTEIN / avidin / AVR4 / high affinity systems / hyper-thermostability
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Avidin / Avidin-related protein 4/5
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLivnah, O. / Eisenberg-Domovich, Y. / Maatta, J.A.E. / Kulomaa, M.S. / Hytonen, V.P. / Nordlund, H.R.
CitationJournal: Biotechnol.Bioeng. / Year: 2011
Title: Chimeric avidin shows stability against harsh chemical conditions-biochemical analysis and 3D structure.
Authors: Maatta, J.A. / Eisenberg-Domovich, Y. / Nordlund, H.R. / Hayouka, R. / Kulomaa, M.S. / Livnah, O. / Hytonen, V.P.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Avidin, Avidin-related protein 4/5
B: Avidin, Avidin-related protein 4/5
C: Avidin, Avidin-related protein 4/5
D: Avidin, Avidin-related protein 4/5
E: Avidin, Avidin-related protein 4/5
F: Avidin, Avidin-related protein 4/5
G: Avidin, Avidin-related protein 4/5
H: Avidin, Avidin-related protein 4/5
I: Avidin, Avidin-related protein 4/5
K: Avidin, Avidin-related protein 4/5
M: Avidin, Avidin-related protein 4/5
N: Avidin, Avidin-related protein 4/5


Theoretical massNumber of molelcules
Total (without water)172,80312
Polymers172,80312
Non-polymers00
Water1,63991
1
A: Avidin, Avidin-related protein 4/5
B: Avidin, Avidin-related protein 4/5
C: Avidin, Avidin-related protein 4/5
D: Avidin, Avidin-related protein 4/5


Theoretical massNumber of molelcules
Total (without water)57,6014
Polymers57,6014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-66 kcal/mol
Surface area18470 Å2
MethodPISA
2
E: Avidin, Avidin-related protein 4/5
F: Avidin, Avidin-related protein 4/5
G: Avidin, Avidin-related protein 4/5
H: Avidin, Avidin-related protein 4/5


Theoretical massNumber of molelcules
Total (without water)57,6014
Polymers57,6014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-65 kcal/mol
Surface area19000 Å2
MethodPISA
3
I: Avidin, Avidin-related protein 4/5
K: Avidin, Avidin-related protein 4/5

I: Avidin, Avidin-related protein 4/5
K: Avidin, Avidin-related protein 4/5


Theoretical massNumber of molelcules
Total (without water)57,6014
Polymers57,6014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area9930 Å2
ΔGint-68 kcal/mol
Surface area18720 Å2
MethodPISA
4
M: Avidin, Avidin-related protein 4/5
N: Avidin, Avidin-related protein 4/5

M: Avidin, Avidin-related protein 4/5
N: Avidin, Avidin-related protein 4/5


Theoretical massNumber of molelcules
Total (without water)57,6014
Polymers57,6014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9630 Å2
ΔGint-72 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.657, 124.791, 88.895
Angle α, β, γ (deg.)90.00, 114.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11K
21N

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 4 - 123 / Label seq-ID: 7 - 124

Dom-IDAuth asym-IDLabel asym-ID
1KJ
2NL

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Components

#1: Protein
Avidin, Avidin-related protein 4/5


Mass: 14400.254 Da / Num. of mol.: 12
Fragment: P02701 Residues 25-61, 85-152 and P56734 residues 62-82
Mutation: I141Y
Source method: isolated from a genetically manipulated source
Details: SEE REMARK 999 FOR CHIMERA ASSEMBLY INFORMATION / Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVR4, AVR5, AVD / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P02701, UniProt: P56734
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS ENTRY IS A CHIMERA OF TWO GENES AVD AND AVR4. THE ASSEMBLY IS EXPRESSION TAG, P02701 25-61, ...THIS ENTRY IS A CHIMERA OF TWO GENES AVD AND AVR4. THE ASSEMBLY IS EXPRESSION TAG, P02701 25-61, P56734 62-82, P02701 85-152

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.3
Details: 20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→94.42 Å / Num. all: 42677 / Num. obs: 42677 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.076 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.63 / % possible all: 90.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AVI

2avi


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.869 / SU B: 40.947 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30929 2141 5 %RANDOM
Rwork0.2218 ---
obs0.22592 40311 98.01 %-
all-40310 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.114 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å2-1.01 Å2
2--5.23 Å20 Å2
3----4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10923 0 0 91 11014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211161
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.791.92315121
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.71551380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18223.631471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.69151849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0651566
X-RAY DIFFRACTIONr_chiral_restr0.1130.21714
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218274
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2650.25518
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.27385
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2440
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.2260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6261.56887
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.158211121
X-RAY DIFFRACTIONr_scbond_it1.46734274
X-RAY DIFFRACTIONr_scangle_it2.4174.54000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: K / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
464TIGHT POSITIONAL0.050.05
435MEDIUM POSITIONAL0.070.5
464TIGHT THERMAL0.160.5
435MEDIUM THERMAL0.232
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 131 -
Rwork0.312 2739 -
obs--90.25 %
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)
12.19330.08810.99560.6226-0.0532.3414-0.005-0.08740.0719-0.02520.094-0.0086-0.2122-0.0518-0.0890.04340.01180.04780.03230.02420.072646.68191.06212.5794
21.1046-0.753-0.45911.96570.24521.0369-0.0750.06230.00090.148-0.07080.09290.1418-0.01830.14580.04480.03030.03320.08140.00020.062666.0621-21.4603-26.9708
30.99720.30490.92250.57490.48891.7874-0.013-0.0281-0.0811-0.10980.06840.12750.1482-0.1793-0.05540.0773-0.0588-0.03880.05680.04030.062695.7977-61.5358-38.9081
40.5571-0.01-0.48151.378-0.21753.7651-0.07110.10120.1023-0.21860.01020.05531.1311-0.31790.06090.4066-0.059-0.01650.1154-0.01340.072875.294641.6295-6.098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 123
2X-RAY DIFFRACTION1B4 - 123
3X-RAY DIFFRACTION1C3 - 123
4X-RAY DIFFRACTION1D3 - 123
5X-RAY DIFFRACTION2E4 - 123
6X-RAY DIFFRACTION2F3 - 123
7X-RAY DIFFRACTION2G3 - 123
8X-RAY DIFFRACTION2H3 - 123
9X-RAY DIFFRACTION3I3 - 123
10X-RAY DIFFRACTION3K3 - 123
11X-RAY DIFFRACTION4M3 - 123
12X-RAY DIFFRACTION4N3 - 123

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