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- PDB-3b83: Computer-Based Redesign of a beta Sandwich Protein Suggests that ... -

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Basic information

Entry
Database: PDB / ID: 3b83
TitleComputer-Based Redesign of a beta Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo beta Sheet Design.
ComponentsTEN-D3
KeywordsUNKNOWN FUNCTION / beta sheet / computational redesigned protein / Cell adhesion / EGF-like domain / Extracellular matrix / Glycoprotein / Phosphorylation / Secreted
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHu, X. / Ke, H. / Kuhlman, B.
CitationJournal: Structure / Year: 2008
Title: Computer-Based Redesign of a beta Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo beta Sheet Design.
Authors: Hu, X. / Wang, H. / Ke, H. / Kuhlman, B.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 5, 2013Group: Structure summary
Revision 1.3Aug 30, 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: TEN-D3
B: TEN-D3
C: TEN-D3
D: TEN-D3
E: TEN-D3
F: TEN-D3
G: TEN-D3
H: TEN-D3


Theoretical massNumber of molelcules
Total (without water)89,1328
Polymers89,1328
Non-polymers00
Water84747
1
A: TEN-D3
C: TEN-D3
E: TEN-D3
F: TEN-D3

A: TEN-D3
C: TEN-D3
E: TEN-D3
F: TEN-D3

A: TEN-D3
C: TEN-D3
E: TEN-D3
F: TEN-D3

A: TEN-D3
C: TEN-D3
E: TEN-D3
F: TEN-D3

B: TEN-D3
D: TEN-D3
G: TEN-D3
H: TEN-D3

B: TEN-D3
D: TEN-D3
G: TEN-D3
H: TEN-D3

B: TEN-D3
D: TEN-D3
G: TEN-D3
H: TEN-D3

B: TEN-D3
D: TEN-D3
G: TEN-D3
H: TEN-D3


Theoretical massNumber of molelcules
Total (without water)356,52732
Polymers356,52732
Non-polymers00
Water57632
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
crystal symmetry operation5_454-x-1/2,y+1/2,-z-11
crystal symmetry operation6_444x-1/2,-y-1/2,-z-11
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_454-y-1,-x,-z-11
Buried area47440 Å2
ΔGint-294 kcal/mol
Surface area138660 Å2
MethodPISA
2
A: TEN-D3
E: TEN-D3


Theoretical massNumber of molelcules
Total (without water)22,2832
Polymers22,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area11070 Å2
MethodPISA
3
B: TEN-D3
G: TEN-D3


Theoretical massNumber of molelcules
Total (without water)22,2832
Polymers22,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-8 kcal/mol
Surface area10710 Å2
MethodPISA
4
C: TEN-D3
F: TEN-D3


Theoretical massNumber of molelcules
Total (without water)22,2832
Polymers22,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-8 kcal/mol
Surface area10550 Å2
MethodPISA
5
D: TEN-D3
H: TEN-D3


Theoretical massNumber of molelcules
Total (without water)22,2832
Polymers22,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.329, 126.329, 134.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
TEN-D3


Mass: 11141.483 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Computationally redesigned variant / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium dihydrogen phosphate, 0.1 M potassium dihydrogen phosphate, 0.1M MES pH 6.5, 2.2M NaCl,100 mM Urea, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 43149 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 1.76 / Num. unique all: 7253 / % possible all: 94.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ten

1ten


Resolution: 2.4→30 Å / Isotropic thermal model: isotropic / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 4145 random
Rwork0.24 --
obs0.2447 41217 -
Displacement parametersBiso mean: 50.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5901 0 0 47 5948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_angle_deg1.5052

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