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- PDB-4r58: Crystal structure of computational designed leucine rich repeats ... -

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Basic information

Entry
Database: PDB / ID: 4r58
TitleCrystal structure of computational designed leucine rich repeats DLRR_A in space group P21
ComponentsLeucine Rich Repeat proteinLeucine-rich repeat
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: 2.4 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 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: Leucine Rich Repeat protein
C: Leucine Rich Repeat protein
D: Leucine Rich Repeat protein


Theoretical massNumber of molelcules
Total (without water)95,5954
Polymers95,5954
Non-polymers00
Water6,287349
1
A: Leucine Rich Repeat protein


Theoretical massNumber of molelcules
Total (without water)23,8991
Polymers23,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucine Rich Repeat protein


Theoretical massNumber of molelcules
Total (without water)23,8991
Polymers23,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leucine Rich Repeat protein


Theoretical massNumber of molelcules
Total (without water)23,8991
Polymers23,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Leucine Rich Repeat protein


Theoretical massNumber of molelcules
Total (without water)23,8991
Polymers23,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.583, 145.006, 57.700
Angle α, β, γ (deg.)90.00, 115.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1 - 220 / Label seq-ID: 1 - 220

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Leucine Rich Repeat protein / Leucine-rich repeat


Mass: 23898.801 Da / Num. of mol.: 4
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 / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 22% PEG 3350, 0.1M MES, 0.2 M NaCl, pH 6.0, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→25.01 Å / Num. all: 35346 / Num. obs: 34180 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rsym value: 0.081 / Net I/σ(I): 24
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.36-2.4436.40.183183.7
2.44-2.546.218.70.1491100

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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: 2.4→25.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.983 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.726 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23309 1658 5.1 %RANDOM
Rwork0.18352 ---
obs0.18603 30991 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.16 Å2
2--0.79 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 0 349 7061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196756
X-RAY DIFFRACTIONr_bond_other_d0.0080.026752
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9799184
X-RAY DIFFRACTIONr_angle_other_deg1.363315548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.85428.63292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.519151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.548154
X-RAY DIFFRACTIONr_chiral_restr0.0910.21188
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027740
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021336
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_it0.8581.2333516
X-RAY DIFFRACTIONr_mcbond_other0.8511.2313515
X-RAY DIFFRACTIONr_mcangle_it1.4661.8394388
X-RAY DIFFRACTIONr_mcangle_other1.3381.734397
X-RAY DIFFRACTIONr_scbond_it0.9781.3363240
X-RAY DIFFRACTIONr_scbond_other0.8671.2533268
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4431.8364832
X-RAY DIFFRACTIONr_long_range_B_refined3.5118.6837207
X-RAY DIFFRACTIONr_long_range_B_other3.5118.6877208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A143470.07
12B143470.07
21A141340.09
22C141340.09
31A139490.09
32D139490.09
41B142710.07
42C142710.07
51B140710.08
52D140710.08
61C139090.09
62D139090.09
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 136 -
Rwork0.208 2282 -
obs--99.22 %
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)
12.92472.0965-0.78123.6484-1.33032.36380.04470.0552-0.2069-0.03060.05150.0240.2543-0.0503-0.09620.06360.029-0.02740.0376-0.00990.0347-58.9262-6.878123.7739
23.71721.99520.95522.78250.30531.46950.2175-0.2328-0.33910.1761-0.0819-0.06820.28730.1134-0.13570.07790.0473-0.02370.07870.01760.0396-40.5638-6.601847.6161
31.86091.6864-1.58352.8474-2.86384.3347-0.04890.08480.27670.13610.07420.0227-0.6349-0.0863-0.02530.188-0.0065-0.02640.1135-0.02090.1207-47.637226.524334.2183
42.67831.892-0.76634.8166-2.09292.9796-0.1047-0.08290.3350.08560.11930.0758-0.3938-0.0743-0.01460.0980.0633-0.03620.1013-0.04460.0569-65.209125.85929.5061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 220
2X-RAY DIFFRACTION2B1 - 220
3X-RAY DIFFRACTION3C1 - 220
4X-RAY DIFFRACTION4D1 - 220

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