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- PDB-5bu7: Crystal structure of an engineered protein that forms nanotubes w... -

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Basic information

Entry
Database: PDB / ID: 5bu7
TitleCrystal structure of an engineered protein that forms nanotubes with tunable diameters
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Metalloprotein / Hemeprotein
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsBrodin, J.D. / Smith, S.J. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-10ER46677 United States
CitationJournal: To be Published
Title: Designed, Helical Protein Nanotubes with Tunable Diameters from a Single Building Block.
Authors: Brodin, J.D. / Smith, S.J. / Tezcan, F.A.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,92111
Polymers23,2302
Non-polymers1,6919
Water1,00956
1
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,84222
Polymers46,4604
Non-polymers3,38218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area11130 Å2
ΔGint-493 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.890, 52.890, 257.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-203-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 106
2010B1 - 106

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11615.114 Da / Num. of mol.: 2
Mutation: T96C, D73H, K77H, R98C, Y101C, K27E, D28K, T31E, R34L, L38A, Q41L, H59R, D66A, V69M, L76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.5 / Details: 50-fold excess of zinc chloride

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.46→85.69 Å / Num. obs: 8104 / % possible obs: 95.1 % / Redundancy: 3.5 % / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→45.8 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.3314 / WRfactor Rwork: 0.2528 / FOM work R set: 0.773 / SU B: 13.14 / SU ML: 0.288 / SU R Cruickshank DPI: 1.152 / SU Rfree: 0.3638 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.152 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2923 369 4.7 %RANDOM
Rwork0.2253 ---
obs0.2284 7513 92.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.19 Å2 / Biso mean: 55.873 Å2 / Biso min: 23.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.84 Å20 Å2
2--0.84 Å20 Å2
3----2.73 Å2
Refinement stepCycle: final / Resolution: 2.46→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 93 56 1765
Biso mean--46.93 43.51 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191738
X-RAY DIFFRACTIONr_bond_other_d0.0030.021640
X-RAY DIFFRACTIONr_angle_refined_deg1.3852.0342368
X-RAY DIFFRACTIONr_angle_other_deg0.93333786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0335210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg50.8362780
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00215304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.651154
X-RAY DIFFRACTIONr_chiral_restr0.090.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022014
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02370
Refine LS restraints NCS

Ens-ID: 1 / Number: 6045 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.461→2.525 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 31 -
Rwork0.281 562 -
all-593 -
obs--96.27 %

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