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- PDB-4r5d: Crystal structure of computational designed leucine rich repeats ... -

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Basic information

Entry
Database: PDB / ID: 4r5d
TitleCrystal structure of computational designed leucine rich repeats DLRR_G3 in space group F222
ComponentsLeucine rich repeat protein
KeywordsDE NOVO PROTEIN / Leucine rich repeat (LRR) protein
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: 2.53 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 21, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5517
Polymers48,0091
Non-polymers5426
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.134, 136.384, 161.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-501-

SO4

21A-655-

HOH

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Components

#1: Protein Leucine rich repeat protein


Mass: 48008.770 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 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: Jan 17, 2014 / Details: mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→30 Å / Num. all: 17735 / Num. obs: 17061 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.067 / Net I/σ(I): 0.153
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.49-2.591.94.10.153184.5
2.59-2.692.85.30.156190.6
2.69-2.823.36.30.15192.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERMRphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→23.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.884 / SU B: 18.819 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.715 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24646 869 5.2 %RANDOM
Rwork0.18129 ---
obs0.18475 15856 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.872 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2--0.85 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.53→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 29 91 3487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193525
X-RAY DIFFRACTIONr_bond_other_d0.0010.023416
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9784812
X-RAY DIFFRACTIONr_angle_other_deg0.85937854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.82326.829164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36715630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.731514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
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_it0.6871.1191813
X-RAY DIFFRACTIONr_mcbond_other0.6811.1161812
X-RAY DIFFRACTIONr_mcangle_it1.1981.672282
X-RAY DIFFRACTIONr_mcangle_other1.1981.6732283
X-RAY DIFFRACTIONr_scbond_it1.0371.2711710
X-RAY DIFFRACTIONr_scbond_other1.0351.271710
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6411.8652531
X-RAY DIFFRACTIONr_long_range_B_refined3.7088.8753833
X-RAY DIFFRACTIONr_long_range_B_other3.6698.813814
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.53→2.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 52 -
Rwork0.234 1002 -
obs--85.83 %
Refinement TLS params.Method: refined / Origin x: 102.8243 Å / Origin y: 170.8948 Å / Origin z: 18.791 Å
111213212223313233
T0.0757 Å20.0436 Å2-0.0311 Å2-0.0643 Å2-0.0011 Å2--0.0352 Å2
L0.6582 °20.0489 °2-0.134 °2-3.2024 °20.4812 °2--0.7569 °2
S0.0686 Å °0.1481 Å °-0.0411 Å °-0.2166 Å °-0.0484 Å °0.0377 Å °0.0495 Å °-0.0069 Å °-0.0202 Å °

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