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- PDB-4hb5: Crystal Structure of Engineered Protein. Northeast Structural Gen... -

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Basic information

Entry
Database: PDB / ID: 4hb5
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR267.
ComponentsEngineered Protein
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / 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 speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.294 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
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
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
B: Engineered Protein


Theoretical massNumber of molelcules
Total (without water)36,9512
Polymers36,9512
Non-polymers00
Water1,67593
1
A: Engineered Protein


Theoretical massNumber of molelcules
Total (without water)18,4751
Polymers18,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Engineered Protein


Theoretical massNumber of molelcules
Total (without water)18,4751
Polymers18,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.977, 45.469, 63.152
Angle α, β, γ (deg.)90.000, 107.170, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer,18.88 kD,98.5%

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Components

#1: Protein Engineered Protein


Mass: 18475.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: OR267-21.1-SeM-R2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 8
Details: 20% PEG 4000, 0.1M magnesium sulfate, 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: 0.97885 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 21, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 27096 / Num. obs: 26798 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 28.07 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 24.5
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 8.8 / Num. unique all: 2694 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GPM

4gpm


Resolution: 2.294→35.537 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1316 4.96 %RANDOM
Rwork0.194 ---
obs0.196 26546 97.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.706 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 104.8 Å2 / Biso mean: 39.025 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.868 Å20 Å25.09 Å2
2---10.693 Å20 Å2
3---12.561 Å2
Refinement stepCycle: LAST / Resolution: 2.294→35.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 0 93 2512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052455
X-RAY DIFFRACTIONf_angle_d1.3753309
X-RAY DIFFRACTIONf_chiral_restr0.09360
X-RAY DIFFRACTIONf_plane_restr0.005450
X-RAY DIFFRACTIONf_dihedral_angle_d17.113947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.294-2.3860.2571200.1942814293498
2.386-2.4940.2551710.18628573028100
2.494-2.6260.2641680.2032792296099
2.626-2.790.3631460.2342707285395
2.79-3.0060.2741420.22428993041100
3.006-3.3080.2471150.21628812996100
3.308-3.7860.2271450.1932731287695
3.786-4.7680.181510.162770292197
4.768-35.5410.2061580.1862779293797
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)
10.3738-0.31590.08750.44240.24720.6694-0.01950.0590.00160.027-0.04740.0517-0.0022-0.0154-00.1043-0.01620.01210.1148-0.02490.121219.8522-0.15346.1475
20.3485-0.0496-0.04430.812-0.58920.2710.01350.01540.0033-0.0922-0.14840.02460.07210.029900.1493-0.0066-0.01380.11950.01790.118619.6181.566336.6574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 158
2X-RAY DIFFRACTION2chain BB2 - 163

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