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

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Basic information

Entry
Database: PDB / ID: 4gmr
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR266.
ComponentsOR266 DE NOVO PROTEIN
KeywordsDE NOVO PROTEIN / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / OR266
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / NITRATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.377 Å
AuthorsVorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Mao, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Mao, 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 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: OR266 DE NOVO PROTEIN
B: OR266 DE NOVO PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4303
Polymers36,3682
Non-polymers621
Water86548
1
A: OR266 DE NOVO PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2462
Polymers18,1841
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OR266 DE NOVO PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,1841
Polymers18,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.114, 43.592, 69.942
Angle α, β, γ (deg.)90.000, 93.100, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer,15.69 kD,93.5%

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Components

#1: Protein OR266 DE NOVO PROTEIN


Mass: 18184.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21, OR266-21.1-NC5a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 40% PEG 1000, 0.1M potassium nitrate, 0.1M HEPES, pH7.5, Microbatch crystallization under oil, 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 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: 2.377→50 Å / Num. all: 24545 / Num. obs: 24422 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 32.67 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.98
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2465 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2XEE chain A

2xee


Resolution: 2.377→42.852 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.74 / Cross valid method: THROUGHOUT / σ(F): 1.2 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1189 4.87 %RANDOM
Rwork0.199 ---
obs0.2 24390 98.42 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.114 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 122.17 Å2 / Biso mean: 39.547 Å2 / Biso min: 10.62 Å2
Baniso -1Baniso -2Baniso -3
1-3.403 Å2-0 Å2-2.739 Å2
2---0.649 Å2-0 Å2
3----2.754 Å2
Refinement stepCycle: LAST / Resolution: 2.377→42.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 4 48 2511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092496
X-RAY DIFFRACTIONf_angle_d1.4113369
X-RAY DIFFRACTIONf_chiral_restr0.096377
X-RAY DIFFRACTIONf_plane_restr0.006459
X-RAY DIFFRACTIONf_dihedral_angle_d16.632942
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 (%)
2.377-2.4850.3421280.2872731285992
2.485-2.6160.3042040.26628833087100
2.616-2.780.31420.25329353077100
2.78-2.9940.2761330.2282931306499
2.994-3.2950.2591650.2232925309099
3.295-3.7720.2431450.1892921306699
3.772-4.7510.1691460.1482929307599
4.751-42.8590.1761260.1692946307299
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)
10.0148-0.00330.00590.0093-0.02020.01920.0064-0.0094-0.0339-0.0182-0.00420.0038-0.08330.011100.12770.0084-0.02370.0896-0.00730.122120.36970.41142.0154
20.0108-0.01480.0135-0.0028-0.01260.03680.09580.20140.05170.0462-0.2030.20120.08470.1106-0-0.168-0.01240.24910.1175-0.0271-0.16266.11-10.7683-29.4152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 168
2X-RAY DIFFRACTION2chain BB2 - 163

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