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- PDB-4f34: Symfoil-4V synthetic protein with T30E/T72E/T116E mutations, and ... -

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Basic information

Entry
Database: PDB / ID: 4f34
TitleSymfoil-4V synthetic protein with T30E/T72E/T116E mutations, and delta His tag
Componentsde novo protein Symfoil-4V
KeywordsUNKNOWN FUNCTION / synthetic de novo / beta-trefoil
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBlaber, M. / Xia, X.
CitationJournal: TO BE PUBLISHED
Title: Symfoil-4V synthetic protein with T30E/T72E/T116E mutations, and delta His tag
Authors: Blaber, M. / Xia, X.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: de novo protein Symfoil-4V
B: de novo protein Symfoil-4V
C: de novo protein Symfoil-4V
D: de novo protein Symfoil-4V


Theoretical massNumber of molelcules
Total (without water)60,4984
Polymers60,4984
Non-polymers00
Water4,990277
1
A: de novo protein Symfoil-4V


Theoretical massNumber of molelcules
Total (without water)15,1241
Polymers15,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: de novo protein Symfoil-4V


Theoretical massNumber of molelcules
Total (without water)15,1241
Polymers15,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: de novo protein Symfoil-4V


Theoretical massNumber of molelcules
Total (without water)15,1241
Polymers15,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: de novo protein Symfoil-4V


Theoretical massNumber of molelcules
Total (without water)15,1241
Polymers15,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.402, 70.300, 122.179
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
de novo protein Symfoil-4V


Mass: 15124.446 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20%(w/v)PEG-3000; 0.1M citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 19, 2012 / Details: Osmic blue confocal mirror
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 36034 / Num. obs: 35169 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.95→2.01 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.559 Å / SU ML: 0.3 / σ(F): 2 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 1754 4.99 %random
Rwork0.1984 ---
obs0.2005 35169 95.67 %-
all-36761 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.715 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.1549 Å2-0 Å20 Å2
2---4.2378 Å2-0 Å2
3---12.3927 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 0 277 4143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083946
X-RAY DIFFRACTIONf_angle_d1.165346
X-RAY DIFFRACTIONf_dihedral_angle_d15.9711528
X-RAY DIFFRACTIONf_chiral_restr0.084587
X-RAY DIFFRACTIONf_plane_restr0.007739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9499-2.00260.34071260.28692403X-RAY DIFFRACTION91
2.0026-2.06140.291320.26162475X-RAY DIFFRACTION94
2.0614-2.12790.35491310.23352508X-RAY DIFFRACTION94
2.1279-2.20390.28381300.21632519X-RAY DIFFRACTION94
2.2039-2.2920.27661320.20232502X-RAY DIFFRACTION95
2.292-2.39610.2541350.19312545X-RAY DIFFRACTION96
2.3961-2.52220.23331310.20472545X-RAY DIFFRACTION96
2.5222-2.67980.2631350.20882556X-RAY DIFFRACTION96
2.6798-2.88620.24111350.20312563X-RAY DIFFRACTION96
2.8862-3.17550.22281360.20372584X-RAY DIFFRACTION96
3.1755-3.63240.22511400.18632673X-RAY DIFFRACTION98
3.6324-4.56690.19021440.16372709X-RAY DIFFRACTION99
4.5669-19.56010.24841470.20422833X-RAY DIFFRACTION99

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