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- PDB-4r80: Crystal Structure of a De Novo Designed Beta Sheet Protein, Cysta... -

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Basic information

Entry
Database: PDB / ID: 4r80
TitleCrystal Structure of a De Novo Designed Beta Sheet Protein, Cystatin Fold, Northeast Structural Genomics Consortium (NESG) Target OR486
ComponentsOR486
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) / Target OR486 / protein engineering / denovo beta sheet design / Cystatin Fold
Function / homologyNuclear Transport Factor 2; Chain: A, - #630 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.445 Å
AuthorsGuan, R. / Marcos, E. / O'Connell, P. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Acton, T.B. / Everett, J.K. / Baker, D. ...Guan, R. / Marcos, E. / O'Connell, P. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Acton, T.B. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of an engineered protein with denovo beta sheet design, Northeast Structural Genomics Consortium (NESG) Target OR486
Authors: Guan, R. / Marcos, E. / O'Connell, P. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Acton, T.B. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: OR486
B: OR486


Theoretical massNumber of molelcules
Total (without water)19,7942
Polymers19,7942
Non-polymers00
Water1,06359
1
A: OR486


Theoretical massNumber of molelcules
Total (without water)9,8971
Polymers9,8971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OR486


Theoretical massNumber of molelcules
Total (without water)9,8971
Polymers9,8971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.139, 70.619, 41.040
Angle α, β, γ (deg.)90.000, 113.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

21A-127-

HOH

31A-133-

HOH

DetailsThe biological molecule is unknown

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Components

#1: Protein OR486


Mass: 9897.169 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), 10mg/ml. Reservoir solution:0.1 M NaH2PO4, 0.1 M Na Acetate, pH 5.5, 28% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97916 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 11, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.445→41.671 Å / Num. all: 5311 / Num. obs: 5311 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 33.87
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.06 / % possible all: 42.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.445→33.818 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.56 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.256 973 9.59 %random
Rwork0.218 ---
obs0.222 5311 94.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.43 Å2 / Biso mean: 27.676 Å2 / Biso min: 6.83 Å2
Refinement stepCycle: LAST / Resolution: 2.445→33.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 0 59 1275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031220
X-RAY DIFFRACTIONf_angle_d0.5841628
X-RAY DIFFRACTIONf_chiral_restr0.043192
X-RAY DIFFRACTIONf_plane_restr0.002212
X-RAY DIFFRACTIONf_dihedral_angle_d12.252504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.445-2.5740.2911040.2361211131586
2.574-2.7350.3281530.2491320147396
2.735-2.9460.3071270.251356148396
2.946-3.2420.2851450.2131308145395
3.242-3.7110.251450.2111326147196
3.711-4.6730.2171630.1861303146696
4.673-33.8210.2031360.2251350148696

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