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- PDB-5aq7: DARPin-based Crystallization Chaperones exploit Molecular Geometr... -

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Basic information

Entry
Database: PDB / ID: 5aq7
TitleDARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
ComponentsD12_DB04V3
KeywordsCHAPERONE / CRYSTALLIZATION CHAPERONE / DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) / RIGID DOMAIN FUSION
Function / homologyAnkyrin repeat-containing domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / MALONATE ION
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 25, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
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
Revision 2.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: D12_DB04V3
B: D12_DB04V3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6154
Polymers90,4112
Non-polymers2042
Water7,963442
1
A: D12_DB04V3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4103
Polymers45,2051
Non-polymers2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D12_DB04V3


Theoretical massNumber of molelcules
Total (without water)45,2051
Polymers45,2051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.040, 156.240, 68.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein D12_DB04V3


Mass: 45205.465 Da / Num. of mol.: 2
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: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.25 Å3/Da / Density % sol: 45.3 % / Description: NONE
Crystal growpH: 7.5
Details: PEG3350 20.0% W/V, SODIUM MALONATE 0.2 M, BIS TRIS PROPANE 0.1M, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 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 Å / Relative weight: 1
ReflectionResolution: 2.1→43.49 Å / Num. obs: 50274 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 34.29 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.59
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.36 / % possible all: 99.3

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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 AND 1SVX CHAIN A

3dtm

1svx


Resolution: 2.1→43.488 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 2514 5 %
Rwork0.1899 --
obs0.1919 50258 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6150 0 14 442 6606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036306
X-RAY DIFFRACTIONf_angle_d0.7148566
X-RAY DIFFRACTIONf_dihedral_angle_d12.3762326
X-RAY DIFFRACTIONf_chiral_restr0.04997
X-RAY DIFFRACTIONf_plane_restr0.0031117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14030.36791370.33132609X-RAY DIFFRACTION99
2.1403-2.1840.34291360.30642582X-RAY DIFFRACTION100
2.184-2.23150.31521380.2852610X-RAY DIFFRACTION100
2.2315-2.28340.31961380.26912621X-RAY DIFFRACTION100
2.2834-2.34050.33361370.25492612X-RAY DIFFRACTION100
2.3405-2.40380.29811390.25232637X-RAY DIFFRACTION100
2.4038-2.47450.3011380.23212631X-RAY DIFFRACTION100
2.4745-2.55440.26351390.22022629X-RAY DIFFRACTION100
2.5544-2.64570.26471380.2132626X-RAY DIFFRACTION100
2.6457-2.75160.23381390.20962637X-RAY DIFFRACTION100
2.7516-2.87680.27981390.21622636X-RAY DIFFRACTION100
2.8768-3.02840.26571390.2172637X-RAY DIFFRACTION100
3.0284-3.21810.27851390.20592653X-RAY DIFFRACTION100
3.2181-3.46650.24331410.1812676X-RAY DIFFRACTION100
3.4665-3.81520.18971410.16072670X-RAY DIFFRACTION100
3.8152-4.36680.1871410.13312694X-RAY DIFFRACTION100
4.3668-5.49990.16991440.14022728X-RAY DIFFRACTION100
5.4999-43.49760.171510.16872856X-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)
11.5765-0.08730.61992.29240.65138.8356-0.0650.1229-0.1404-0.20350.01130.26690.1586-0.12210.0470.2898-0.0219-0.00640.2881-0.00650.4061-25.57245.9434-54.7317
21.46540.20061.04222.28420.11913.25440.01940.11190.02350.21460.0918-0.0481-0.24570.2342-0.09850.3690.0460.01920.2879-0.02270.2855-11.521725.6411-11.1449
31.917-0.32361.01012.94520.89321.97240.02580.2317-0.1318-0.01070.1063-0.02880.03160.3459-0.13590.32010.03710.06390.3881-0.00430.2279-11.947319.7746-21.1223
42.1827-0.3057-2.40221.33230.6155.1623-0.2434-0.0146-0.3244-0.0744-0.0882-0.12310.6536-0.10710.28260.5955-0.11530.0870.3874-0.03440.405-28.598966.7269-12.0766
51.4777-0.2737-0.94195.07672.91063.36670.02260.13590.0901-0.1106-0.30350.4382-0.1511-0.34370.21260.3987-0.0214-0.00330.3273-0.03620.3268-11.864645.3061-47.0838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 13 THROUGH 170 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 171 THROUGH 285 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 286 THROUGH 418 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 13 THROUGH 170 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 171 THROUGH 418 )

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