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- PDB-4m6a: N-Terminal beta-Strand Swapping in a Consensus Derived Alternativ... -

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Basic information

Entry
Database: PDB / ID: 4m6a
TitleN-Terminal beta-Strand Swapping in a Consensus Derived Alternative Scaffold Driven by Stabilizing Hydrophobic Interactions
ComponentsTencon
KeywordsDE NOVO PROTEIN / Tencon / FN3-like domain / alternative scaffold / b-strand swapping
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsLuo, J. / Teplyakov, A. / Obmolova, G. / Malia, T.J. / Chan, W. / Jocobs, S.A. / O'neil, K.T. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: N-terminal beta-strand swapping in a consensus-derived alternative scaffold driven by stabilizing hydrophobic interactions.
Authors: Luo, J. / Teplyakov, A. / Obmolova, G. / Malia, T.J. / Chan, W. / Jacobs, S.A. / O'Neil, K.T. / Gilliland, G.L.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tencon
B: Tencon
C: Tencon
D: Tencon
E: Tencon
F: Tencon
G: Tencon
H: Tencon
I: Tencon
J: Tencon


Theoretical massNumber of molelcules
Total (without water)99,02010
Polymers99,02010
Non-polymers00
Water3,279182
1
A: Tencon
B: Tencon


Theoretical massNumber of molelcules
Total (without water)19,8042
Polymers19,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-28 kcal/mol
Surface area9200 Å2
MethodPISA
2
C: Tencon
D: Tencon


Theoretical massNumber of molelcules
Total (without water)19,8042
Polymers19,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-27 kcal/mol
Surface area9280 Å2
MethodPISA
3
E: Tencon
F: Tencon


Theoretical massNumber of molelcules
Total (without water)19,8042
Polymers19,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-26 kcal/mol
Surface area9270 Å2
MethodPISA
4
G: Tencon
H: Tencon


Theoretical massNumber of molelcules
Total (without water)19,8042
Polymers19,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-24 kcal/mol
Surface area9300 Å2
MethodPISA
5
I: Tencon
J: Tencon


Theoretical massNumber of molelcules
Total (without water)19,8042
Polymers19,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-26 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.370, 41.880, 128.180
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tencon


Mass: 9901.954 Da / Num. of mol.: 10 / Fragment: FN3-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate buffer, pH 4.6, 25% PEG 4K, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 15, 2007
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→35 Å / Num. all: 25822 / Num. obs: 23524 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.4
Reflection shellResolution: 2.7→2.8 Å / % possible all: 60.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: dev_896)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3tes

3tes


Resolution: 2.71→35 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 31.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 1231 5.23 %random
Rwork0.2322 ---
obs0.2353 23524 91.15 %-
all-23524 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.739 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.5361 Å20 Å26.8747 Å2
2--1.9326 Å2-0 Å2
3----9.4687 Å2
Refinement stepCycle: LAST / Resolution: 2.71→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6675 0 0 182 6857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026819
X-RAY DIFFRACTIONf_angle_d0.5499305
X-RAY DIFFRACTIONf_dihedral_angle_d11.3212425
X-RAY DIFFRACTIONf_chiral_restr0.0351078
X-RAY DIFFRACTIONf_plane_restr0.0031204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.81990.38361110.33111759X-RAY DIFFRACTION66
2.8199-2.94820.37911180.32422209X-RAY DIFFRACTION82
2.9482-3.10350.43231500.3162441X-RAY DIFFRACTION92
3.1035-3.29780.39661370.2782585X-RAY DIFFRACTION96
3.2978-3.55230.30361270.23092637X-RAY DIFFRACTION96
3.5523-3.90930.29781630.23332610X-RAY DIFFRACTION97
3.9093-4.4740.30371400.21472631X-RAY DIFFRACTION97
4.474-5.6330.2351400.18452678X-RAY DIFFRACTION98
5.633-35.04870.19181450.20342743X-RAY DIFFRACTION96

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