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- PDB-3pg0: Crystal structure of designed 3-fold symmetric protein, ThreeFoil -

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Basic information

Entry
Database: PDB / ID: 3pg0
TitleCrystal structure of designed 3-fold symmetric protein, ThreeFoil
ComponentsThreeFoil
KeywordsDE NOVO PROTEIN / symmetric design / Beta-trefoil / engineered module / sugar binding
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Function and homology information
Biological speciesArtificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLobsanov, Y.D. / Broom, A. / Howell, P.L. / Rose, D.R. / Meiering, E.M.
CitationJournal: Structure / Year: 2012
Title: Modular evolution and the origins of symmetry: reconstruction of a three-fold symmetric globular protein.
Authors: Broom, A. / Doxey, A.C. / Lobsanov, Y.D. / Berthin, L.G. / Rose, D.R. / Howell, P.L. / McConkey, B.J. / Meiering, E.M.
History
DepositionOct 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: ThreeFoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8967
Polymers18,0611
Non-polymers8356
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.012, 45.012, 113.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-156-

HOH

21A-251-

HOH

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Components

#1: Protein ThreeFoil


Mass: 18061.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: formed inclusion bodies / Source: (gene. exp.) Artificial gene (others) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.59 Å3/Da / Density % sol: 22.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0 M ammonium sulfate, 0.1 M bis-tris, protein concentration = 7 mg/mL, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→35.26 Å / Num. all: 15533 / Num. obs: 15533 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.25 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.62-1.684.290.3633.5196
1.68-1.756.280.3174.41100
1.75-1.826.440.2455.91100
1.82-1.926.490.1997.31100
1.92-2.046.480.1539.51100
2.04-2.26.590.11311.9199.9
2.2-2.426.530.08116.1199.9
2.42-2.776.590.07218199.6
2.77-3.496.570.05821.5199.9
3.49-35.266.180.03832.8199.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.6Ddata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
BALBESphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KNM

1knm


Resolution: 1.62→35.258 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.21 / σ(F): 1.37 / Phase error: 15.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 1086 7 %
Rwork0.166 --
obs0.1673 15504 99.52 %
all-15497 -
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.856 Å2 / ksol: 0.421 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4738 Å2-0 Å2-0 Å2
2---1.4738 Å20 Å2
3---2.9475 Å2
Refinement stepCycle: LAST / Resolution: 1.62→35.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 55 115 1247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061235
X-RAY DIFFRACTIONf_angle_d1.0741677
X-RAY DIFFRACTIONf_dihedral_angle_d21.086496
X-RAY DIFFRACTIONf_chiral_restr0.074166
X-RAY DIFFRACTIONf_plane_restr0.004219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.69370.34051280.35271700X-RAY DIFFRACTION97
1.6937-1.7830.29011330.231771X-RAY DIFFRACTION100
1.783-1.89470.19541340.15061776X-RAY DIFFRACTION100
1.8947-2.0410.16991330.14511775X-RAY DIFFRACTION100
2.041-2.24640.19221350.16261786X-RAY DIFFRACTION100
2.2464-2.57140.18991360.15941801X-RAY DIFFRACTION100
2.5714-3.23930.17111380.15511846X-RAY DIFFRACTION100
3.2393-35.26680.15271490.15261963X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.64080.1579-0.65510.8867-1.10464.943-0.2010.21490.1077-0.0659-0.08990.06080.4150.23840.270.11160.0142-0.02080.2591-0.02510.066522.714-8.3927-2.5334
20.3030.1052-0.01780.0716-0.0080.1017-0.04920.00750.0186-0.0088-0.0018-0.0127-0.02110.03290.02520.0733-0.0038-0.0140.07940.00520.081615.1133-4.35016.8016
30.02160.03490.04130.33060.06770.1253-0.03610.0392-0.0231-0.01250.02040.0640.0249-0.08040.01240.0709-0.02630.01360.1273-0.01030.11520.7118-9.3332.8813
40.12270.01750.05350.41650.21660.38690.0213-0.00930.0146-0.1182-0.10530.03320.0001-0.14050.06850.12610.0026-0.00940.1371-0.01490.100717.5892-19.2264-1.7556
50.5612-0.4013-0.01550.3143-0.05050.2674-0.0287-0.0541-0.12640.05020.02530.07780.04130.0410.00210.08630.00610.00570.07590.00780.087710.7048-18.52248.9354
60.31410.31250.06830.6340.32690.23610.04370.0261-0.0322-0.0361-0.07820.0188-0.05340.02150.03110.12320.0036-0.01940.1318-0.00470.12778.4045-13.392-9.6128
71.0885-0.15870.26760.03790.0010.21190.08480.1595-0.1828-0.04080.00360.0012-0.0143-0.0138-0.05230.08280.01220.01380.1074-0.01680.12068.2272-13.7974-5.2484
80.7557-0.1280.14920.3664-0.10620.1155-0.0380.0726-0.08590.01850.02390.0477-0.01460.01670.00540.0634-0.0045-0.00340.07610.00130.05853.0924-8.11152.264
90.354-0.60690.12171.70010.7111.3259-0.0458-0.17770.0485-0.14920.3628-0.0996-0.08860.2444-0.31050.0665-0.04540.01880.1888-0.00650.137718.6743-6.279-6.15
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:6)
2X-RAY DIFFRACTION2(chain A and resid 7:39)
3X-RAY DIFFRACTION3(chain A and resid 40:43)
4X-RAY DIFFRACTION4(chain A and resid 44:57)
5X-RAY DIFFRACTION5(chain A and resid 58:89)
6X-RAY DIFFRACTION6(chain A and resid 90:96)
7X-RAY DIFFRACTION7(chain A and resid 97:104)
8X-RAY DIFFRACTION8(chain A and resid 105:136)
9X-RAY DIFFRACTION9(chain A and resid 137:141)

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