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

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Basic information

Entry
Database: PDB / ID: 4ijb
TitleCrystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR288
ComponentsEngineered Protein OR288
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Engineered Protein
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.739 Å
AuthorsVorobiev, S. / Su, M. / Bick, M.J. / Seetharaman, J. / Khare, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Day, A. / Everett, J.K. ...Vorobiev, S. / Su, M. / Bick, M.J. / Seetharaman, J. / Khare, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Day, A. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Hunt, J. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Engineered Protein OR288.
Authors: Vorobiev, S. / Su, M. / Bick, M.J. / Seetharaman, J. / Khare, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Day, A. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Hunt, J. / Tong, L.
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Structure summary
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engineered Protein OR288


Theoretical massNumber of molelcules
Total (without water)29,8581
Polymers29,8581
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.319, 60.187, 110.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer,26.36 kD,97.4%

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Components

#1: Protein Engineered Protein OR288


Mass: 29858.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: OR288-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 6.5
Details: 30% PEG 8000, 0.2M sodium acetate, 0.1M sodium cacodylate, pH 6.5, Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.739→40.58 Å / Num. all: 46740 / Num. obs: 46740 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.8
Reflection shellResolution: 1.739→1.85 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
NE-CATRemote Accessdata collection
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.739→25.499 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.41 / σ(F): 1.21 / Phase error: 18.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 2401 5.14 %
Rwork0.1843 --
obs0.1851 46732 99.97 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.591 Å2 / ksol: 0.428 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.419 Å20 Å2-0 Å2
2--4.8031 Å2-0 Å2
3----1.3841 Å2
Refinement stepCycle: LAST / Resolution: 1.739→25.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 0 178 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092007
X-RAY DIFFRACTIONf_angle_d1.4712705
X-RAY DIFFRACTIONf_dihedral_angle_d13.723794
X-RAY DIFFRACTIONf_chiral_restr0.101309
X-RAY DIFFRACTIONf_plane_restr0.006347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7395-1.7750.37431360.35742618X-RAY DIFFRACTION100
1.775-1.81360.30851530.31592570X-RAY DIFFRACTION100
1.8136-1.85570.26091160.27122671X-RAY DIFFRACTION100
1.8557-1.90210.26941320.23692564X-RAY DIFFRACTION100
1.9021-1.95350.21631400.19762644X-RAY DIFFRACTION100
1.9535-2.0110.17921500.19072583X-RAY DIFFRACTION100
2.011-2.07590.2031600.18442617X-RAY DIFFRACTION100
2.0759-2.150.21691530.19112567X-RAY DIFFRACTION100
2.15-2.23610.191470.17152607X-RAY DIFFRACTION100
2.2361-2.33780.181480.17252621X-RAY DIFFRACTION100
2.3378-2.46090.19571610.1772560X-RAY DIFFRACTION100
2.4609-2.6150.20081370.17592627X-RAY DIFFRACTION100
2.615-2.81660.18891390.17682606X-RAY DIFFRACTION100
2.8166-3.09970.2141500.17462603X-RAY DIFFRACTION100
3.0997-3.54720.19281120.16692650X-RAY DIFFRACTION100
3.5472-4.46510.16361450.15222609X-RAY DIFFRACTION100
4.4651-25.50220.18611220.1842614X-RAY DIFFRACTION100

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