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- PDB-4pq8: Crystal Structure of Engineered Protein, Northeast Structural Gen... -

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Basic information

Entry
Database: PDB / ID: 4pq8
TitleCrystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR465
ComponentsDESIGNED PROTEIN OR465
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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: 1.833 Å
AuthorsVorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. / Baker, D. ...Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Engineered Protein OR465.
Authors: Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_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: DESIGNED PROTEIN OR465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1132
Polymers30,0781
Non-polymers351
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.914, 72.914, 51.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Detailsmonomer,31.3 kD,96.8%

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Components

#1: Protein DESIGNED PROTEIN OR465


Mass: 30077.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: OR465-15.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 45.77 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization cocktail: 40% PEG 4000, 0.1M potassium phosphate monobasic, 0.1M MES, pH 6.0, Microbatch ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization cocktail: 40% PEG 4000, 0.1M potassium phosphate monobasic, 0.1M MES, pH 6.0, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 23943 / Num. obs: 23751 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 16.46 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 48.6
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 10 / Num. unique all: 2367 / % possible all: 92

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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: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RFJ

3rfj


Resolution: 1.833→41.97 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 16.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2367 5.14 %RANDOM
Rwork0.154 ---
obs0.155 23730 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.025 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 84.82 Å2 / Biso mean: 22.045 Å2 / Biso min: 5.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.983 Å20 Å2-0 Å2
2--1.983 Å2-0 Å2
3----3.967 Å2
Refinement stepCycle: LAST / Resolution: 1.833→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 1 315 2184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061889
X-RAY DIFFRACTIONf_angle_d1.3842577
X-RAY DIFFRACTIONf_chiral_restr0.102329
X-RAY DIFFRACTIONf_plane_restr0.005334
X-RAY DIFFRACTIONf_dihedral_angle_d13.834701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.833-1.870.221290.1782274240388
1.87-1.9110.2371330.18825802713100
1.911-1.9550.2081660.17725552721100
1.955-2.0040.21430.15325832726100
2.004-2.0580.1961450.15526362781100
2.058-2.1190.1911260.1525762702100
2.119-2.1870.2011650.14525442709100
2.187-2.2660.2161390.14325952734100
2.266-2.3560.1671270.14226082735100
2.356-2.4640.1911220.15226082730100
2.464-2.5930.171550.1525852740100
2.593-2.7560.1821240.15226072731100
2.756-2.9680.1711680.15825532721100
2.968-3.2670.1771410.16125992740100
3.267-3.740.1531360.15525812717100
3.74-4.7110.141110.13426352746100
4.711-41.9810.1621370.16325842721100
Refinement TLS params.Method: refined / Origin x: 36.5882 Å / Origin y: 10.4612 Å / Origin z: 0.0628 Å
111213212223313233
T0.025 Å2-0.0173 Å2-0.0041 Å2--0.0593 Å20.0638 Å2---0.0233 Å2
L0.0008 °20.0012 °20.0016 °2-0.0043 °2-0.0072 °2--0.0092 °2
S0.0326 Å °0.0074 Å °0.0211 Å °-0.0238 Å °-0.0201 Å °-0.0187 Å °0.0249 Å °-0.0122 Å °-0 Å °
Refinement TLS groupSelection details: chain A

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