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- PDB-4j29: Crystal Structure of Engineered Protein. Northeast Structural Gen... -

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Basic information

Entry
Database: PDB / ID: 4j29
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR258.
ComponentsEngineered Protein OR258
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / NESG / OR258 / Northeast Structural Genomics Consortium
Function / homologyRossmann fold - #11230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsVorobiev, S. / Su, M. / Koga, R. / Seetharaman, J. / Koga, N. / Mao, L. / Xiao, R. / Kohan, E. / Castelllanos, J. / Everett, J.K. ...Vorobiev, S. / Su, M. / Koga, R. / Seetharaman, J. / Koga, N. / Mao, L. / Xiao, R. / Kohan, E. / Castelllanos, J. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Engineered Protein OR258.
Authors: Vorobiev, S. / Su, M. / Koga, R. / Seetharaman, J. / Koga, N. / Mao, L. / Xiao, R. / Kohan, E. / Castelllanos, J. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 OR258


Theoretical massNumber of molelcules
Total (without water)15,8631
Polymers15,8631
Non-polymers00
Water28816
1
A: Engineered Protein OR258

A: Engineered Protein OR258


Theoretical massNumber of molelcules
Total (without water)31,7262
Polymers31,7262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5520 Å2
ΔGint-44 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.558, 67.558, 48.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-212-

HOH

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Components

#1: Protein Engineered Protein OR258


Mass: 15862.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b+, OR258-29.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.76 Å3/Da / Density % sol: 30.07 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP

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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: 2.1→50 Å / Num. all: 12677 / Num. obs: 12646 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.6 % / Biso Wilson estimate: 36.16 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 22.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 28.5 % / Rmerge(I) obs: 1.87 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1663 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→23.885 Å / Occupancy max: 1 / Occupancy min: 0.88 / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.44 / Stereochemistry target values: ML
Details: IN THE CRYSTAL STRUCTURE OR258 FORMS DIMER WITH CRYSTAL SYMMETRY MATE (-X+1,-Y+1,Z) BY DOMAIN SWAPPING.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 593 4.69 %RANDOM
Rwork0.237 ---
obs0.239 12634 99.95 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.951 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 104.57 Å2 / Biso mean: 46.611 Å2 / Biso min: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.275 Å20 Å2-0 Å2
2--2.275 Å2-0 Å2
3----4.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 0 16 1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111044
X-RAY DIFFRACTIONf_angle_d1.2581401
X-RAY DIFFRACTIONf_chiral_restr0.094169
X-RAY DIFFRACTIONf_plane_restr0.004181
X-RAY DIFFRACTIONf_dihedral_angle_d17.096426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.3110.3451590.29230023161
2.311-2.6450.2671620.26329863148
2.645-3.3310.2881380.25130293167
3.331-23.8870.2431340.21430243158
Refinement TLS params.Method: refined / Origin x: 34.5346 Å / Origin y: 25.6132 Å / Origin z: 12.4845 Å
111213212223313233
T0.2804 Å2-0.0117 Å20.0338 Å2-0.2428 Å20.0045 Å2--0.2587 Å2
L1.1917 °2-0.9876 °2-0.4079 °2-1.2539 °2-0.0062 °2--1.1222 °2
S-0.2437 Å °0.0605 Å °-0.1524 Å °0.2844 Å °0.0726 Å °0.1568 Å °0.159 Å °-0.0696 Å °0.1081 Å °
Refinement TLS groupSelection details: chain A

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