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- PDB-5aqb: DARPin-based Crystallization Chaperones exploit Molecular Geometr... -

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Basic information

Entry
Database: PDB / ID: 5aqb
TitleDARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
Components
  • 3G61_DB15V4
  • GREEN FLUORESCENT PROTEIN
KeywordsCHAPERONE / CRYSTALLIZATION CHAPERONE / DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) / RIGID DOMAIN FUSION
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesSYNTHETIC CONSTRUCT (others)
AEQUOREA VICTORIA (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsBatyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Darpin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
Authors: Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A.
History
DepositionSep 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3G61_DB15V4
B: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)72,3182
Polymers72,3182
Non-polymers00
Water12,917717
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-6.4 kcal/mol
Surface area31460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)90.150, 96.170, 92.780
Angle α, β, γ (deg.)90.00, 118.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2093-

HOH

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Components

#1: Protein 3G61_DB15V4


Mass: 46254.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE
#2: Protein GREEN FLUORESCENT PROTEIN


Mass: 26063.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE / References: UniProt: P42212
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 46.8 % / Description: NONE
Crystal growpH: 8.5
Details: PEG3350 20.0% W/V, SODIUM FORMATE 0.2 M, BIS TRIS PROPANE 0.1 M, PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2012 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.37→48.08 Å / Num. obs: 143759 / % possible obs: 99 % / Observed criterion σ(I): 1.09 / Redundancy: 6.6 % / Biso Wilson estimate: 20.21 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 5.8 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3DTM, 1SVX CHAIN A AND 1GFL

3dtm

1svx

1gfl


Resolution: 1.37→48.085 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 7178 5 %
Rwork0.1564 --
obs0.1574 143449 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.86 Å2
Refinement stepCycle: LAST / Resolution: 1.37→48.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 0 717 5648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085294
X-RAY DIFFRACTIONf_angle_d0.9857239
X-RAY DIFFRACTIONf_dihedral_angle_d13.0882021
X-RAY DIFFRACTIONf_chiral_restr0.078826
X-RAY DIFFRACTIONf_plane_restr0.007952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.38550.44272040.42163770X-RAY DIFFRACTION83
1.3855-1.40180.44032260.40014304X-RAY DIFFRACTION94
1.4018-1.41890.39462350.37154463X-RAY DIFFRACTION99
1.4189-1.43690.34662440.33024637X-RAY DIFFRACTION100
1.4369-1.45580.3192380.31754523X-RAY DIFFRACTION100
1.4558-1.47570.26782420.27444585X-RAY DIFFRACTION100
1.4757-1.49680.24632430.26124612X-RAY DIFFRACTION100
1.4968-1.51920.25492380.23114529X-RAY DIFFRACTION100
1.5192-1.54290.27792390.22114538X-RAY DIFFRACTION100
1.5429-1.56820.23222420.2074596X-RAY DIFFRACTION100
1.5682-1.59530.18972410.19744582X-RAY DIFFRACTION100
1.5953-1.62430.20642390.18534538X-RAY DIFFRACTION100
1.6243-1.65550.19312430.17234611X-RAY DIFFRACTION100
1.6555-1.68930.18952420.17394607X-RAY DIFFRACTION100
1.6893-1.7260.19022390.16934531X-RAY DIFFRACTION100
1.726-1.76620.18212390.16174538X-RAY DIFFRACTION100
1.7662-1.81040.17252430.16064616X-RAY DIFFRACTION100
1.8104-1.85930.17162380.15544527X-RAY DIFFRACTION100
1.8593-1.9140.1852390.15064569X-RAY DIFFRACTION100
1.914-1.97580.1552430.14354611X-RAY DIFFRACTION100
1.9758-2.04640.17122430.14444607X-RAY DIFFRACTION100
2.0464-2.12840.16062400.14294571X-RAY DIFFRACTION100
2.1284-2.22520.17792410.14324575X-RAY DIFFRACTION100
2.2252-2.34250.16792400.13754555X-RAY DIFFRACTION100
2.3425-2.48930.14762410.13844578X-RAY DIFFRACTION100
2.4893-2.68150.16562420.13784603X-RAY DIFFRACTION100
2.6815-2.95130.16062430.14654609X-RAY DIFFRACTION100
2.9513-3.37830.16622410.14514578X-RAY DIFFRACTION100
3.3783-4.25580.14722430.13654625X-RAY DIFFRACTION100
4.2558-48.11460.17612470.14734683X-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)
11.58922.8820.37636.63831.18580.2621-0.53840.10870.58710.08880.00630.3514-1.3064-0.1268-0.07220.90420.1218-0.25340.347-0.00470.415815.779124.59293.0257
20.9252-1.3081.36921.1013-2.09993.4430.02120.0133-0.0354-0.0295-0.0813-0.0697-0.0480.06960.02920.26140.0248-0.0560.2264-0.02330.232425.5476104.657911.9341
30.9372-0.18250.37191.1796-0.09220.9843-0.0029-0.0369-0.02480.0089-0.00960.033-0.0132-0.03870.030.1346-0.00820.01070.1536-0.00370.167147.770578.368434.1749
41.34310.19010.41041.23190.02372.07550.00680.1472-0.004-0.0833-0.0093-0.08750.00960.1607-0.00030.19010.04550.01040.1974-0.01340.171413.2102102.9367-23.6286
51.58160.30140.42631.09830.02841.79280.05210.001-0.05770.0166-0.0162-0.140.12040.15610.00490.1590.0563-0.00650.1614-0.00780.155516.5428100.6355-12.8791
60.74320.06790.69470.55440.03361.0161-0.07260.13890.0821-0.04670.0267-0.0946-0.1010.2427-0.01670.19890.0205-0.00080.2397-0.00950.207916.3525108.8703-17.0378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 18 THROUGH 49 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 50 THROUGH 180 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 181 THROUGH 428 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 68 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 69 THROUGH 187 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 188 THROUGH 231 )

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