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- PDB-4lpt: Crystal structure of monomeric TENCON variant P54CR4-31 -

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Basic information

Entry
Database: PDB / ID: 4lpt
TitleCrystal structure of monomeric TENCON variant P54CR4-31
ComponentsTENCON variant P54CR4-31
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: 2.544 Å
AuthorsTeplyakov, A. / Obmolova, G. / 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 / 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

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Assembly

Deposited unit
A: TENCON variant P54CR4-31
B: TENCON variant P54CR4-31
C: TENCON variant P54CR4-31
D: TENCON variant P54CR4-31
E: TENCON variant P54CR4-31
F: TENCON variant P54CR4-31


Theoretical massNumber of molelcules
Total (without water)68,3026
Polymers68,3026
Non-polymers00
Water2,972165
1
A: TENCON variant P54CR4-31


Theoretical massNumber of molelcules
Total (without water)11,3841
Polymers11,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TENCON variant P54CR4-31


Theoretical massNumber of molelcules
Total (without water)11,3841
Polymers11,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TENCON variant P54CR4-31


Theoretical massNumber of molelcules
Total (without water)11,3841
Polymers11,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TENCON variant P54CR4-31


Theoretical massNumber of molelcules
Total (without water)11,3841
Polymers11,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: TENCON variant P54CR4-31


Theoretical massNumber of molelcules
Total (without water)11,3841
Polymers11,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: TENCON variant P54CR4-31


Theoretical massNumber of molelcules
Total (without water)11,3841
Polymers11,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.520, 64.130, 194.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TENCON variant P54CR4-31


Mass: 11383.629 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M acetate, pH 4.5, 19% PEG8000, 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: Jun 3, 2010 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.544→29 Å / Num. all: 21214 / Num. obs: 21214 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.544→2.61 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.321 / % possible all: 83.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBE ENTRY 3TES

3tes


Resolution: 2.544→15 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.862 / SU B: 11.704 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.691 / ESU R Free: 0.334 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27517 1083 5 %RANDOM
Rwork0.19701 ---
all0.20112 20013 --
obs0.20112 20013 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2---0.42 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.544→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4237 0 0 165 4402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224336
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9685926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67224.682173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39515631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2981511
X-RAY DIFFRACTIONr_chiral_restr0.0790.2693
X-RAY DIFFRACTIONr_gen_planes_refined00.0213283
X-RAY DIFFRACTIONr_mcbond_it3.74322784
X-RAY DIFFRACTIONr_mcangle_it6.65944482
X-RAY DIFFRACTIONr_scbond_it37.721881552
X-RAY DIFFRACTIONr_scangle_it41.419881444
LS refinement shellResolution: 2.544→2.608 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 70 -
Rwork0.279 1177 -
obs--100 %

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