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- PDB-4lpv: Crystal structure of TENCON variant P41BR3-42 -

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Basic information

Entry
Database: PDB / ID: 4lpv
TitleCrystal structure of TENCON variant P41BR3-42
ComponentsTENCON variant P41BR3-42
KeywordsDE NOVO PROTEIN / fibronectin type III fold / alternate scaffold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTeplyakov, A. / Obmolova, G. / Luo, J. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: C-terminal beta-strand swapping in a consensus-derived fibronectin Type III scaffold.
Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Jacobs, S.A. / Chan, W. / Domingo, D. / Baker, A. / O'Neil, K.T. / Gilliland, G.L.
History
DepositionJul 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TENCON variant P41BR3-42
B: TENCON variant P41BR3-42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0213
Polymers21,8992
Non-polymers1221
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-27 kcal/mol
Surface area10890 Å2
MethodPISA
2
A: TENCON variant P41BR3-42
B: TENCON variant P41BR3-42
hetero molecules

A: TENCON variant P41BR3-42
B: TENCON variant P41BR3-42
hetero molecules

A: TENCON variant P41BR3-42
B: TENCON variant P41BR3-42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0629
Polymers65,6966
Non-polymers3663
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20810 Å2
ΔGint-104 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.460, 106.460, 115.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1001-

TRS

21A-1001-

TRS

31A-1227-

HOH

41B-237-

HOH

51B-238-

HOH

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Components

#1: Protein TENCON variant P41BR3-42


Mass: 10949.251 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 5.74 Å3/Da / Density % sol: 78.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 1.35 M ammonium sulfate, 5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 9, 2009 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→49 Å / Num. all: 42629 / Num. obs: 42629 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.369 / % possible all: 62.8

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Processing

Software
NameVersionClassification
StructureStudiodata 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: 1.8→31.1 Å / σ(F): 2 / Phase error: 21.16 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 2037 4.8 %RANDOM
Rwork0.1637 ---
obs0.1638 42629 94.8 %-
all-42629 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.965 Å2 / ksol: 0.427 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8283 Å20 Å2-0 Å2
2--1.8283 Å2-0 Å2
3----3.6567 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 8 364 1811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071487
X-RAY DIFFRACTIONf_angle_d1.1782031
X-RAY DIFFRACTIONf_dihedral_angle_d15.058523
X-RAY DIFFRACTIONf_chiral_restr0.075237
X-RAY DIFFRACTIONf_plane_restr0.006257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84970.2858940.26731958X-RAY DIFFRACTION61
1.8497-1.89970.28751100.25772417X-RAY DIFFRACTION75
1.8997-1.95560.26761380.23372769X-RAY DIFFRACTION86
1.9556-2.01870.23911450.2252974X-RAY DIFFRACTION93
2.0187-2.09090.22231460.20983046X-RAY DIFFRACTION95
2.0909-2.17460.21261490.19313045X-RAY DIFFRACTION95
2.1746-2.27350.22021490.19443057X-RAY DIFFRACTION95
2.2735-2.39330.21121500.1813056X-RAY DIFFRACTION95
2.3933-2.54320.20891490.18343038X-RAY DIFFRACTION95
2.5432-2.73950.17681480.16313070X-RAY DIFFRACTION95
2.7395-3.01490.20881490.15113034X-RAY DIFFRACTION95
3.0149-3.45070.17551540.13763069X-RAY DIFFRACTION95
3.4507-4.34570.1541520.11513033X-RAY DIFFRACTION95
4.3457-31.170.16121550.14993052X-RAY DIFFRACTION95

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