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Basic information

Entry
Database: PDB / ID: 4hxt
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR329
ComponentsDe Novo Protein OR329
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsVorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, X. / Lee, D. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, X. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: NAT.CHEM. / Year: 2017
Title: Computational design of self-assembling cyclic protein homo-oligomers.
Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D.
History
DepositionNov 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De Novo Protein OR329


Theoretical massNumber of molelcules
Total (without water)26,0731
Polymers26,0731
Non-polymers00
Water3,333185
1
A: De Novo Protein OR329

A: De Novo Protein OR329


Theoretical massNumber of molelcules
Total (without water)52,1462
Polymers52,1462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2070 Å2
ΔGint-13 kcal/mol
Surface area20280 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.493, 31.941, 72.543
Angle α, β, γ (deg.)90.000, 90.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

Detailsmonomer,24.69 kD,83.5%|dimer,49.94 kD,14.2%

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Components

#1: Protein De Novo Protein OR329


Mass: 26073.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: OR329-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 4.2
Details: 20% PEG 8000, 0.1M magnesium nitrate, 0.1M sodium citrate, pH 4.2, Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 31075 / Num. obs: 28434 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.86 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 25.7
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3132 / % possible all: 58.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 4DB8

4db8


Resolution: 1.95→40.13 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1399 4.92 %RANDOM
Rwork0.164 ---
obs0.166 28422 90.9 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.714 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 95.73 Å2 / Biso mean: 31.63 Å2 / Biso min: 12.93 Å2
Baniso -1Baniso -2Baniso -3
1--3.541 Å20 Å2-1.729 Å2
2--6.182 Å2-0 Å2
3----2.641 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 0 185 1959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051786
X-RAY DIFFRACTIONf_angle_d0.9182423
X-RAY DIFFRACTIONf_chiral_restr0.074313
X-RAY DIFFRACTIONf_plane_restr0.002314
X-RAY DIFFRACTIONf_dihedral_angle_d14.148659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.020.2171040.2031638174254
2.02-2.1010.2211230.1842114223772
2.101-2.1970.2351280.1732506263485
2.197-2.3120.1931500.1542944309499
2.312-2.4570.1821380.16329803118100
2.457-2.6470.2241290.16630093138100
2.647-2.9130.2271480.18129703118100
2.913-3.3350.2111520.18329533105100
3.335-4.2010.1531720.13829713143100
4.201-40.1390.1741550.1642938309399

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