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

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Basic information

Entry
Database: PDB / ID: 4gpm
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR264.
ComponentsEngineered Protein OR264
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsVorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: NAT.CHEM. / Year: 2017
Title: Computational design of self-assembling cyclic protein homo-oligomers.
Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Engineered Protein OR264
B: Engineered Protein OR264


Theoretical massNumber of molelcules
Total (without water)36,7052
Polymers36,7052
Non-polymers00
Water3,189177
1
A: Engineered Protein OR264


Theoretical massNumber of molelcules
Total (without water)18,3521
Polymers18,3521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Engineered Protein OR264


Theoretical massNumber of molelcules
Total (without water)18,3521
Polymers18,3521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.086, 56.824, 105.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,19.62 kD,98.7%

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Components

#1: Protein Engineered Protein OR264


Mass: 18352.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21, OR264-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.97 Å3/Da / Density % sol: 37.41 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 9
Details: 40% PEG 1000, 0.1M lithium chloride, 0.1M TAPS, pH 9.0 , Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 37872 / Num. obs: 35751 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.73 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.4
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3 / Num. unique all: 3796 / % possible all: 80.3

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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 2XEE, chain A

2xee


Resolution: 2.002→30.139 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0.65 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1808 5.08 %RANDOM
Rwork0.176 ---
obs0.177 35590 94.59 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.481 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso max: 80.64 Å2 / Biso mean: 27.95 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.206 Å20 Å2-0 Å2
2--3.477 Å2-0 Å2
3----4.683 Å2
Refinement stepCycle: LAST / Resolution: 2.002→30.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 0 177 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052384
X-RAY DIFFRACTIONf_angle_d1.1943209
X-RAY DIFFRACTIONf_chiral_restr0.088363
X-RAY DIFFRACTIONf_plane_restr0.006436
X-RAY DIFFRACTIONf_dihedral_angle_d14.531903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.002-2.0560.261010.1982262236382
2.056-2.1170.1871450.1862507265291
2.117-2.1850.2251190.182570268991
2.185-2.2630.2641170.1932537265493
2.263-2.3540.2561710.1752520269193
2.354-2.4610.2361400.1762573271393
2.461-2.5910.2111500.1842558270895
2.591-2.7530.2321650.1912665283097
2.753-2.9650.261510.1962669282098
2.965-3.2630.2351400.1912720286099
3.263-3.7350.1671480.1642745289399
3.735-4.7020.1311300.14127352865100
4.702-30.1420.1831310.1842721285298
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00750.02590.04850.2848-0.07590.1892-0.03110.0137-0.01310.00910.0401-0.03150.0061-0.07770.07450.0263-0.00890.08510.00160.076125.566622.762177.026
20.3155-0.1053-0.03290.2287-0.0120.1526-0.01910.0324-0.0009-0.0160.0260.02680.0112-0.03330.0469-0.0243-0.02410.0480.0060.05481.799230.717976.1968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 158
2X-RAY DIFFRACTION2chain BB3 - 159

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