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- PDB-4r6f: Crystal structure of computational designed protein DLRR_I -

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Basic information

Entry
Database: PDB / ID: 4r6f
TitleCrystal structure of computational designed protein DLRR_I
ComponentsLeucine rich repeat DLRR_I
KeywordsDE NOVO PROTEIN / Leucine rich motifs
Function / homologyLeucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsShen, B.W. / Stoddard, B.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Control of repeat-protein curvature by computational protein design.
Authors: Park, K. / Shen, B.W. / Parmeggiani, F. / Huang, P.S. / Stoddard, B.L. / Baker, D.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 18, 2015Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine rich repeat DLRR_I


Theoretical massNumber of molelcules
Total (without water)36,5291
Polymers36,5291
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.135, 42.571, 67.607
Angle α, β, γ (deg.)90.00, 102.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Leucine rich repeat DLRR_I


Mass: 36529.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24% PEG 3350, 0.1 M HEPES, 0.2 M Ammonium Sulfate, 0.1 M Proline, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Apr 15, 2014 / Details: mirrors
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→66.1 Å / Num. all: 32346 / Num. obs: 31150 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Rsym value: 0.076 / Net I/σ(I): 33.7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.73-1.7924.70.205184.1
1.79-1.862.66.90.164187.7
1.86-1.95312.70.134190.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERMRphasing
REFMAC5.8.0071refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational designed template

Resolution: 1.73→66.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.129 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20388 1540 5.1 %RANDOM
Rwork0.15638 ---
obs0.15875 28848 94.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.703 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.8 Å2
2--0.46 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.73→66.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 0 261 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192615
X-RAY DIFFRACTIONr_bond_other_d0.0010.022555
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9683568
X-RAY DIFFRACTIONr_angle_other_deg0.96535860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.2426.942121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.913157
X-RAY DIFFRACTIONr_chiral_restr0.1240.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1411.6821325
X-RAY DIFFRACTIONr_mcbond_other2.1181.6791324
X-RAY DIFFRACTIONr_mcangle_it3.1132.5141658
X-RAY DIFFRACTIONr_mcangle_other1.881.4051659
X-RAY DIFFRACTIONr_scbond_it3.1532.0751290
X-RAY DIFFRACTIONr_scbond_other1.8731.1741293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9071.6731914
X-RAY DIFFRACTIONr_long_range_B_refined5.58.5273019
X-RAY DIFFRACTIONr_long_range_B_other5.3798.1812955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 77 -
Rwork0.206 1875 -
obs--82.75 %

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