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

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Basic information

Entry
Database: PDB / ID: 4rzp
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium (NESG) Target OR366.
ComponentsEngineered Protein OR366
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Engineered Protein / OR366
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsVorobiev, S. / Parmeggiani, F. / Dimaio, F. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kogan, S. / Everett, J.K. / Acton, T.B. / Baker, D. ...Vorobiev, S. / Parmeggiani, F. / Dimaio, F. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kogan, S. / 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 OR366
Authors: Vorobiev, S. / Parmeggiani, F. / Dimaio, F. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kogan, S. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Source and taxonomy
Revision 1.2Sep 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: Engineered Protein OR366
B: Engineered Protein OR366


Theoretical massNumber of molelcules
Total (without water)54,1702
Polymers54,1702
Non-polymers00
Water1,29772
1
A: Engineered Protein OR366


Theoretical massNumber of molelcules
Total (without water)27,0851
Polymers27,0851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Engineered Protein OR366


Theoretical massNumber of molelcules
Total (without water)27,0851
Polymers27,0851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint1 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.718, 81.256, 97.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,22.89 kD,62.4%|monomer,21.3 kD,23.6%

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Components

#1: Protein Engineered Protein OR366


Mass: 27085.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG, OR366-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 277 K / Method: microbatch under paraffin oil / pH: 5.8
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 27% PEG 3350, 0.1M MES pH 5.8, 5% w/v 1-butyl-2,3-dimethylimidazolium tetrafluoroborate, ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 27% PEG 3350, 0.1M MES pH 5.8, 5% w/v 1-butyl-2,3-dimethylimidazolium tetrafluoroborate, microbatch under paraffin oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97947 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 28, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 23566 / Num. obs: 23566 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 62.13 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 13.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2342 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HXT

4hxt


Resolution: 2.804→41.716 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1152 4.99 %RANDOM
Rwork0.193 ---
obs0.197 23089 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.18 Å2 / Biso mean: 63.773 Å2 / Biso min: 29.43 Å2
Refinement stepCycle: LAST / Resolution: 2.804→41.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 0 72 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093621
X-RAY DIFFRACTIONf_angle_d1.2554888
X-RAY DIFFRACTIONf_chiral_restr0.045600
X-RAY DIFFRACTIONf_plane_restr0.005657
X-RAY DIFFRACTIONf_dihedral_angle_d16.9791359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.804-2.9320.3161310.2422811294299
2.932-3.0860.3491580.25927562914100
3.086-3.280.3311770.24727862963100
3.28-3.5330.2781550.23127832938100
3.533-3.8880.3171310.2262441257288
3.888-4.450.2751270.1512794292199
4.45-5.6050.1991500.1722749289999
5.605-41.720.2171230.1652817294099
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)
10.17940.06630.53530.1963-0.06831.7865-0.02030.0043-0.0357-0.0089-0.0371-0.03680.01130.001700.35850.01440.0070.3608-0.00060.3821-8.6871-7.004617.3712
20.7837-0.28260.3351.0042-0.27271.5108-0.06740.0173-0.0140.0189-0.00720.00420.0159-0.0899-00.31510.00210.01510.3385-0.00550.3438-24.3803-4.736838.1822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 242
2X-RAY DIFFRACTION2chain BB1 - 242

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