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

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Basic information

Entry
Database: PDB / ID: 4hhu
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR280.
ComponentsOR280
KeywordsStructural Genomics / Unknown Function / Engineered Protein / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyRibosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsVorobiev, S. / Lew, S. / Lin, Y.-R. / Seetharaman, J. / Castelllanos, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Koga, N. / Koga, R. ...Vorobiev, S. / Lew, S. / Lin, Y.-R. / Seetharaman, J. / Castelllanos, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Koga, N. / Koga, R. / 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 OR280.
Authors: Vorobiev, S. / Lew, S. / Lin, Y.-R. / Seetharaman, J. / Castelllanos, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Koga, N. / Koga, R. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. ...Authors: Vorobiev, S. / Lew, S. / Lin, Y.-R. / Seetharaman, J. / Castelllanos, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Koga, N. / Koga, R. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: OR280
B: OR280
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6365
Polymers38,9812
Non-polymers6553
Water2,540141
1
A: OR280
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7572
Polymers19,4901
Non-polymers2661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OR280
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8793
Polymers19,4901
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.426, 63.623, 81.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,24.34 kD,92.8%

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Components

#1: Protein OR280


Mass: 19490.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: OR280-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Chemical ChemComp-AE4 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.94 Å3/Da / Density % sol: 36.44 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 8
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization cocktail: 80% PEG 400, 0.1M Magnesium chloride, 0.1M Tris-HCl, pH 8.0., Microbatch crystallization ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization cocktail: 80% PEG 400, 0.1M Magnesium chloride, 0.1M Tris-HCl, pH 8.0., Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97904 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 39520 / Num. obs: 39441 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 19.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3955 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→31.812 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0.82 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2002 5.12 %RANDOM
Rwork0.193 ---
obs0.194 39064 98.91 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.014 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 142.73 Å2 / Biso mean: 30.69 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.633 Å2-0 Å20 Å2
2---2.159 Å20 Å2
3---3.792 Å2
Refinement stepCycle: LAST / Resolution: 2→31.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 44 141 2814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012697
X-RAY DIFFRACTIONf_angle_d1.2843604
X-RAY DIFFRACTIONf_chiral_restr0.092418
X-RAY DIFFRACTIONf_plane_restr0.004457
X-RAY DIFFRACTIONf_dihedral_angle_d17.1061051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.3021530.2462582273596
2.05-2.1050.2361500.222639278999
2.105-2.1670.2381690.2072638280799
2.167-2.2370.2861540.2052632278699
2.237-2.3170.211450.2022655280099
2.317-2.410.2351510.22656280799
2.41-2.520.2491620.1932608277099
2.52-2.6520.2511190.2052674279399
2.652-2.8180.2691440.1972632277699
2.818-3.0360.2021280.1982693282199
3.036-3.3410.2071310.1962656278799
3.341-3.8240.2051200.17626772797100
3.824-4.8150.1711590.1552639279899
4.815-31.8160.1791170.2122681279899
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)
10.0172-0.0081-0.02880.01320.01590.03090.20020.0592-0.02720.0607-0.11870.129-0.0631-0.1364-0-0.1314-0.1253-0.1929-0.242-0.2466-0.28570.801136.802837.8951
20.0015-0.0404-0.05740.05650.00640.0540.0410.1796-0.1426-0.12070.11280.14050.0587-0.137300.08640.0436-0.01490.0748-0.06960.068616.42330.127720.9725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 170
2X-RAY DIFFRACTION2chain BB1 - 166

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