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- PDB-9bwn: Nanoparticle Crystal Structure of a Thermostabilized Mutant Rv149... -

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Basic information

Entry
Database: PDB / ID: 9bwn
TitleNanoparticle Crystal Structure of a Thermostabilized Mutant Rv1498A Flavoprotein from Mycobacterium tuberculosis
ComponentsFlavoprotein
KeywordsFLAVOPROTEIN / nanoparticle
Function / homology: / Dodecin / Dodecin-like superfamily / Dodecin / Dodecin-like / Conserved protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsSeraj, N. / Cappelli, L. / Wahome, N. / Cinelli, P. / Fabiola, G. / Cartocci, E. / Delany, I. / Cozzi, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: In silico Self-assembling Protein Nanoparticles Optimization for Protein Antigen display
Authors: Cappelli, L. / Wahome, N. / Cinelli, P. / Giusti, F. / Seraj, N. / Cartocci, E. / Harshbarger, W. / Delany, I. / Cozzi, R.
History
DepositionMay 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavoprotein


Theoretical massNumber of molelcules
Total (without water)8,7571
Polymers8,7571
Non-polymers00
Water00
1
A: Flavoprotein
x 12


Theoretical massNumber of molelcules
Total (without water)105,08112
Polymers105,08112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554-z,-x+1/2,y-1/21
crystal symmetry operation10_555-y+1/2,z+1/2,-x1
crystal symmetry operation27_554-x+1/2,y,-z-1/21
crystal symmetry operation30_555z+1/2,-x+1/2,-y1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation50_555-x+1/2,-y+1/2,z1
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation76_554x,-y+1/2,-z-1/21
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation84_554-y+1/2,-z,x-1/21
Buried area28390 Å2
ΔGint-106 kcal/mol
Surface area35420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.183, 139.183, 139.183
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Space group name HallF4d23
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+1/4
#3: x+1/4,z+1/4,-y+1/4
#4: z+1/4,y+1/4,-x+1/4
#5: -z+1/4,y+1/4,x+1/4
#6: -y+1/4,x+1/4,z+1/4
#7: y+1/4,-x+1/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y+1/4,x+1/4,-z+1/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+1/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x,y+1/2,z+1/2
#26: x+1/4,-z+3/4,y+3/4
#27: x+1/4,z+3/4,-y+3/4
#28: z+1/4,y+3/4,-x+3/4
#29: -z+1/4,y+3/4,x+3/4
#30: -y+1/4,x+3/4,z+3/4
#31: y+1/4,-x+3/4,z+3/4
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y+1/4,x+3/4,-z+3/4
#44: -y+1/4,-x+3/4,-z+3/4
#45: z+1/4,-y+3/4,x+3/4
#46: -z+1/4,-y+3/4,-x+3/4
#47: -x+1/4,z+3/4,y+3/4
#48: -x+1/4,-z+3/4,-y+3/4
#49: x+1/2,y,z+1/2
#50: x+3/4,-z+1/4,y+3/4
#51: x+3/4,z+1/4,-y+3/4
#52: z+3/4,y+1/4,-x+3/4
#53: -z+3/4,y+1/4,x+3/4
#54: -y+3/4,x+1/4,z+3/4
#55: y+3/4,-x+1/4,z+3/4
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+3/4,x+1/4,-z+3/4
#68: -y+3/4,-x+1/4,-z+3/4
#69: z+3/4,-y+1/4,x+3/4
#70: -z+3/4,-y+1/4,-x+3/4
#71: -x+3/4,z+1/4,y+3/4
#72: -x+3/4,-z+1/4,-y+3/4
#73: x+1/2,y+1/2,z
#74: x+3/4,-z+3/4,y+1/4
#75: x+3/4,z+3/4,-y+1/4
#76: z+3/4,y+3/4,-x+1/4
#77: -z+3/4,y+3/4,x+1/4
#78: -y+3/4,x+3/4,z+1/4
#79: y+3/4,-x+3/4,z+1/4
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+3/4,x+3/4,-z+1/4
#92: -y+3/4,-x+3/4,-z+1/4
#93: z+3/4,-y+3/4,x+1/4
#94: -z+3/4,-y+3/4,-x+1/4
#95: -x+3/4,z+3/4,y+1/4
#96: -x+3/4,-z+3/4,-y+1/4

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Components

#1: Protein Flavoprotein


Mass: 8756.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1498A / Production host: Escherichia coli (E. coli) / References: UniProt: I6XY36
Has protein modificationN

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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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Lithium sulfate, 0.1 M Phosphate/citrate pH 4.2, 20% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→41.97 Å / Num. obs: 2334 / % possible obs: 90.71 % / Redundancy: 5.7 % / Biso Wilson estimate: 60.94 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.035 / Rrim(I) all: 0.088 / Net I/σ(I): 34.2
Reflection shellResolution: 3.012→3.79 Å / Num. unique obs: 1029 / CC1/2: 0.462 / CC star: 0.795 / % possible all: 83.05

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Cootmodel building
XDSdata reduction
PHENIX1.20.1_4487phasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→41.97 Å / SU ML: 0.3205 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2913 234 10.03 %
Rwork0.2696 2100 -
obs0.2717 2334 90.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.35 Å2
Refinement stepCycle: LAST / Resolution: 3.01→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 0 0 590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141602
X-RAY DIFFRACTIONf_angle_d1.5303814
X-RAY DIFFRACTIONf_chiral_restr0.070390
X-RAY DIFFRACTIONf_plane_restr0.0046107
X-RAY DIFFRACTIONf_dihedral_angle_d17.8399209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.790.28811030.2717926X-RAY DIFFRACTION83.05
3.79-41.970.29261310.26871174X-RAY DIFFRACTION97.83

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