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- PDB-3qa9: Crystal Structure of Prb (PH1109 protein redesigned for binding) -

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Basic information

Entry
Database: PDB / ID: 3qa9
TitleCrystal Structure of Prb (PH1109 protein redesigned for binding)
ComponentsCoA binding domain protein
KeywordsPROTEIN BINDING / DE NOVO PROTEIN / Prb monomer / CoA binding motif / engineered binding partner for Pdar / Pdar
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSpiegel, P.C.
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 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Feb 21, 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

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Assembly

Deposited unit
A: CoA binding domain protein


Theoretical massNumber of molelcules
Total (without water)17,3981
Polymers17,3981
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.003, 59.395, 60.038
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 CoA binding domain protein


Mass: 17398.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10 mg/mL, 0.1 M Na-acetate, 3.0 M NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→60 Å / Num. all: 11771 / Num. obs: 11519 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 8.1 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→60 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2417 1189 RANDOM
Rwork0.2132 --
all-11771 -
obs-11519 -
Refinement stepCycle: LAST / Resolution: 1.9→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 0 85 1239

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