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- PDB-4r6j: Crystal structure of computaional designed Lucine rich repeats DL... -

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Basic information

Entry
Database: PDB / ID: 4r6j
TitleCrystal structure of computaional designed Lucine rich repeats DLRR_H in space group P212121
ComponentsLucine rich repeats DLRR_H
KeywordsDE NOVO PROTEIN / Leucine rich repeats
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
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 / _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: Lucine rich repeats DLRR_H
B: Lucine rich repeats DLRR_H
C: Lucine rich repeats DLRR_H
D: Lucine rich repeats DLRR_H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1786
Polymers111,9864
Non-polymers1922
Water1086
1
A: Lucine rich repeats DLRR_H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0932
Polymers27,9971
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lucine rich repeats DLRR_H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0932
Polymers27,9971
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lucine rich repeats DLRR_H


Theoretical massNumber of molelcules
Total (without water)27,9971
Polymers27,9971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lucine rich repeats DLRR_H


Theoretical massNumber of molelcules
Total (without water)27,9971
Polymers27,9971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.775, 96.498, 136.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1 - 2531 - 253
21THRTHRBB1 - 2531 - 253
12THRTHRAA1 - 2531 - 253
22THRTHRCC1 - 2531 - 253
13LEULEUAA1 - 2511 - 251
23LEULEUDD1 - 2511 - 251
14THRTHRBB1 - 2531 - 253
24THRTHRCC1 - 2531 - 253
15LEULEUBB1 - 2511 - 251
25LEULEUDD1 - 2511 - 251
16LEULEUCC1 - 2511 - 251
26LEULEUDD1 - 2511 - 251

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Lucine rich repeats DLRR_H


Mass: 27996.521 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 3350, 300 mM ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 27148 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rsym value: 0.092 / Net I/σ(I): 17.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.529 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERMRphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / SU B: 41.03 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25637 1378 5.1 %RANDOM
Rwork0.21889 ---
obs0.22078 25484 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.553 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20 Å2
2--0.66 Å20 Å2
3----3.84 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7865 0 10 6 7881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.027983
X-RAY DIFFRACTIONr_bond_other_d0.0080.027838
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.97510880
X-RAY DIFFRACTIONr_angle_other_deg1.535317988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07251005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.99127.253364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.485151419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5271516
X-RAY DIFFRACTIONr_chiral_restr0.0770.21348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219187
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021765
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_it1.983.1874038
X-RAY DIFFRACTIONr_mcbond_other1.983.1874037
X-RAY DIFFRACTIONr_mcangle_it3.2634.7795037
X-RAY DIFFRACTIONr_mcangle_other3.1054.4995023
X-RAY DIFFRACTIONr_scbond_it2.5563.4873945
X-RAY DIFFRACTIONr_scbond_other2.2213.2513925
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.724.7785811
X-RAY DIFFRACTIONr_long_range_B_refined6.52228.35432744
X-RAY DIFFRACTIONr_long_range_B_other6.52228.35332741
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)
11A155050.12
12B155050.12
21A156790.1
22C156790.1
31A152120.15
32D152120.15
41B154460.13
42C154460.13
51B148130.16
52D148130.16
61C149790.16
62D149790.16
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 99 -
Rwork0.325 1843 -
obs--99.79 %
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)
16.03662.22982.572.460.94522.415-0.18370.110.1433-0.03790.08410.13020.085-0.10280.09960.05040.03820.00750.2863-0.00950.0140.1349-25.8222-14.0958
21.2655-0.40861.30730.9741-0.79117.86040.02460.19140.0824-0.1851-0.1076-0.3656-0.10620.77260.0830.34590.04460.17380.2239-0.00470.216815.3893-15.6248-48.5333
38.02531.7941-0.88752.4983-0.23142.65690.1301-0.33480.24040.4018-0.19660.2675-0.2016-0.13110.06650.28870.1954-0.04870.2478-0.1040.10710.08448.0436-20.1286
43.9098-1.1801-2.07832.62691.96467.147-0.31330.0133-0.2105-0.1333-0.29240.54530.1129-1.80490.60570.29410.04470.07060.8409-0.25880.5615-21.9585-4.3302-39.5161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 253
2X-RAY DIFFRACTION2B1 - 253
3X-RAY DIFFRACTION3C1 - 253
4X-RAY DIFFRACTION4D1 - 252

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