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Basic information

Entry
Database: PDB / ID: 4psj
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium (NESG) Target OR464.
ComponentsOR464
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Engineered Protein / NESG / OR464 / Northeast Structural Genomics Consortium
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: 1.992 Å
AuthorsVorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / 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 OR464.
Authors: Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OR464


Theoretical massNumber of molelcules
Total (without water)29,8941
Polymers29,8941
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.916, 51.455, 69.005
Angle α, β, γ (deg.)90.000, 90.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein OR464


Mass: 29894.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: OR464-15.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.9 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 5.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 25% PEG 3350, 0.1M Bis-Tris, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 29867 / Num. obs: 28015 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.48 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2940 / % possible all: 68.1

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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: 1.992→31.911 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1403 5.03 %RANDOM
Rwork0.181 ---
obs0.184 27919 93.15 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.167 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso max: 84.96 Å2 / Biso mean: 33.483 Å2 / Biso min: 10.91 Å2
Baniso -1Baniso -2Baniso -3
1--2.016 Å2-0 Å2-5.342 Å2
2---6.724 Å20 Å2
3---8.74 Å2
Refinement stepCycle: LAST / Resolution: 1.992→31.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 0 169 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072012
X-RAY DIFFRACTIONf_angle_d1.0542747
X-RAY DIFFRACTIONf_chiral_restr0.067346
X-RAY DIFFRACTIONf_plane_restr0.004360
X-RAY DIFFRACTIONf_dihedral_angle_d17.075755
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 (%)
1.992-2.0640.2681160.2091795191165
2.064-2.1460.2861020.2042295239779
2.146-2.2440.3031670.1952666283394
2.244-2.3620.2581420.2082780292299
2.362-2.510.2831560.19428432999100
2.51-2.7040.2791490.19428743023100
2.704-2.9760.2241420.18328442986100
2.976-3.4060.2231510.17928332984100
3.406-4.2890.2011400.1552831297198
4.289-31.9150.2421380.1742755289397
Refinement TLS params.Method: refined / Origin x: 7.3419 Å / Origin y: 0.571 Å / Origin z: 7.0469 Å
111213212223313233
T0.1085 Å2-0.0267 Å2-0.0279 Å2-0.1253 Å2-0.0103 Å2--0.1746 Å2
L1.4273 °2-0.5281 °2-0.3768 °2-2.3103 °20.4658 °2--1.9631 °2
S0.033 Å °-0.087 Å °-0.0082 Å °0.1957 Å °0.0115 Å °0.026 Å °-0.0014 Å °-0.0058 Å °-0.0489 Å °
Refinement TLS groupSelection details: chain A

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