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- PDB-3q9n: In silico and in vitro co-evolution of a high affinity complement... -

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Basic information

Entry
Database: PDB / ID: 3q9n
TitleIn silico and in vitro co-evolution of a high affinity complementary protein-protein interface
Components
  • CoA binding protein
  • consensus ankyrin repeat
KeywordsPROTEIN BINDING / DE NOVO PROTEIN / Structural Genomics / Israel Structural Proteomics Center / ISPC / Prb-binding designed ankyrin repeat
Function / homology
Function and homology information


Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARBAMOYL SARCOSINE / COENZYME A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKaranicolas, J. / Corn, J.E. / Chen, I. / Joachimiak, L.A. / Dym, O. / Chung, S. / Albeck, S. / Unger, T. / Hu, W. / Liu, G. ...Karanicolas, J. / Corn, J.E. / Chen, I. / Joachimiak, L.A. / Dym, O. / Chung, S. / Albeck, S. / Unger, T. / Hu, W. / Liu, G. / Delbecq, S. / Montelione, G.T. / Spiegel, C. / Liu, D. / Baker, D. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Mol.Cell / Year: 2011
Title: A de novo protein binding pair by computational design and directed evolution.
Authors: Karanicolas, J. / Corn, J.E. / Chen, I. / Joachimiak, L.A. / Dym, O. / Peck, S.H. / Albeck, S. / Unger, T. / Hu, W. / Liu, G. / Delbecq, S. / Montelione, G.T. / Spiegel, C.P. / Liu, D.R. / Baker, D.
History
DepositionJan 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Sep 13, 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 / 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: CoA binding protein
B: CoA binding protein
C: consensus ankyrin repeat
D: consensus ankyrin repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1197
Polymers65,4524
Non-polymers1,6673
Water4,972276
1
A: CoA binding protein
C: consensus ankyrin repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6264
Polymers32,7262
Non-polymers9002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-6 kcal/mol
Surface area13510 Å2
MethodPISA
2
B: CoA binding protein
D: consensus ankyrin repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4943
Polymers32,7262
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-9 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.122, 56.556, 56.977
Angle α, β, γ (deg.)89.78, 112.42, 90.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CoA binding protein


Mass: 16237.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein consensus ankyrin repeat


Mass: 16488.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CMS / CARBAMOYL SARCOSINE


Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 292 K / pH: 6
Details: 0.2 M LiCl 0.1 M MES, PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→37.06 Å / Num. obs: 40222 / % possible obs: 98 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2D59, 1MJO

2d59

1mjo


Resolution: 2→37.06 Å / SU ML: 0.29 / σ(F): 1.98 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 2026 5.04 %
Rwork0.19 --
obs0.192 40212 97.1 %
all-41421 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.45 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2109 Å20.2089 Å2-0.1189 Å2
2--0.2794 Å2-0.1482 Å2
3----0.0685 Å2
Refinement stepCycle: LAST / Resolution: 2→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 105 276 4905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084719
X-RAY DIFFRACTIONf_angle_d1.1196434
X-RAY DIFFRACTIONf_dihedral_angle_d19.6391777
X-RAY DIFFRACTIONf_chiral_restr0.083735
X-RAY DIFFRACTIONf_plane_restr0.015831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0006-2.05060.2951240.22732334X-RAY DIFFRACTION82
2.0506-2.1060.31181500.20842745X-RAY DIFFRACTION97
2.106-2.1680.2951490.20322677X-RAY DIFFRACTION97
2.168-2.2380.27111320.20632752X-RAY DIFFRACTION98
2.238-2.31790.26471520.18752732X-RAY DIFFRACTION98
2.3179-2.41070.2571440.19342763X-RAY DIFFRACTION98
2.4107-2.52040.2681470.20112768X-RAY DIFFRACTION98
2.5204-2.65330.27041160.20362789X-RAY DIFFRACTION98
2.6533-2.81950.23091550.20442749X-RAY DIFFRACTION98
2.8195-3.0370.25511620.21422733X-RAY DIFFRACTION99
3.037-3.34250.2481610.21242804X-RAY DIFFRACTION99
3.3425-3.82570.20611460.1782777X-RAY DIFFRACTION99
3.8257-4.81840.20151390.14422796X-RAY DIFFRACTION99
4.8184-37.06790.18941490.15432767X-RAY DIFFRACTION99
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)
11.1229-0.0740.00970.5512-0.24740.5004-0.02830.0469-0.0193-0.0220.0346-0.03480.01750.019-00.0590.0093-0.00730.0925-0.00990.08832.462518.1166-6.4474
20.73880.45060.08212.13440.1541.2456-0.06790.04250.1089-0.01340.12480.388-0.1374-0.08240.08190.1070.0173-0.00830.09810.04140.1434-35.4042-7.9589.1611
31.0315-0.2645-0.40420.86750.09380.58080.08410.17240.0014-0.0596-0.08490.0211-0.019-0.005100.0890.00790.0020.14940.00190.0976-20.786624.789-9.487
40.2307-0.1676-0.04850.85160.29040.6501-0.04370.01970.05440.03190.0417-0.1746-0.04920.1137-00.2226-0.0464-0.00050.1588-0.01460.1316-16.247-14.473622.8675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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