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- PDB-4qcc: Structure of a cube-shaped, highly porous protein cage designed b... -

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Basic information

Entry
Database: PDB / ID: 4qcc
TitleStructure of a cube-shaped, highly porous protein cage designed by fusing symmetric oligomeric domains
Components2-dehydro-3-deoxy-6-phosphogalactonate aldolase, peptidyl-prolyl cis-trans isomerase chimera
KeywordsSTRUCTURAL PROTEIN / LYASE / protein design / bionanotechnology / self-assembly / symmetry / porous biomaterials
Function / homology2-dehydro-3-deoxy-6-phosphogalactonate aldolase / D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase-type TIM barrel / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 7.078 Å
AuthorsLai, Y.-T. / Yeates, T.O.
CitationJournal: Nat Chem / Year: 2014
Title: Structure of a designed protein cage that self-assembles into a highly porous cube.
Authors: Lai, Y.T. / Reading, E. / Hura, G.L. / Tsai, K.L. / Laganowsky, A. / Asturias, F.J. / Tainer, J.A. / Robinson, C.V. / Yeates, T.O.
History
DepositionMay 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, peptidyl-prolyl cis-trans isomerase chimera
B: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, peptidyl-prolyl cis-trans isomerase chimera


Theoretical massNumber of molelcules
Total (without water)62,4672
Polymers62,4672
Non-polymers00
Water00
1
A: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, peptidyl-prolyl cis-trans isomerase chimera
B: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, peptidyl-prolyl cis-trans isomerase chimera
x 12


Theoretical massNumber of molelcules
Total (without water)749,60324
Polymers749,60324
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation16_544x,-y-1/2,-z-1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation27_554-x+1/2,y,-z-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
crystal symmetry operation33_554y+1/2,z,x-1/21
crystal symmetry operation38_545-x+1/2,-y-1/2,z1
crystal symmetry operation41_545z+1/2,x-1/2,y1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
Buried area75510 Å2
ΔGint-603 kcal/mol
Surface area274240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.680, 272.680, 272.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 5 - 274 / Label seq-ID: 5 - 274

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, peptidyl-prolyl cis-trans isomerase chimera / designed porous protein cube


Mass: 31233.459 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dgoA, fkpA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6BF16, UniProt: U6NBA4, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Sequence detailsPROTEIN IS A DESIGNED CHIMERA COMPRISING RESIDUES 1-203 OF UNP Q6BF16 AND RESIDUES 45-116 OF UNP ...PROTEIN IS A DESIGNED CHIMERA COMPRISING RESIDUES 1-203 OF UNP Q6BF16 AND RESIDUES 45-116 OF UNP U6NBA4 CONNECTED BY A QKQKEQRQ LINKER.

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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: 6.76 Å3/Da / Density % sol: 81.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, pH 6.0, 0.6 M ammonium sulfate, 1% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 5, 2014
RadiationMonochromator: Varimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 7.078→96.407 Å / Num. obs: 2526 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 320.857 Å2 / Rmerge(I) obs: 0.073 / Χ2: 0.894 / Net I/σ(I): 15.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
7.078-7.260.7121.6761419595.1
7.26-7.460.3443.3768018097.8
7.46-7.680.2175.5763816696.5
7.68-7.910.254.9465718098.4
7.91-8.170.225.4862216996.6
8.17-8.460.1736.9963216897.7
8.46-8.780.12210.4660215795.7
8.78-9.140.10511.7256515096.2
9.14-9.540.11210.9152914295.9
9.54-10.010.04922.6849713295
10.01-10.550.03825.7447212994.2
10.55-11.190.03726.1648112896.2
11.19-11.960.04225.3242511693.5
11.96-12.920.04126.6140010795.5
12.92-14.160.03327.373509795.1
14.16-15.830.03131.243579896.1
15.83-18.280.02637.113048194.2
18.28-22.380.02539.542496994.5
22.38-31.660.02845.551694571.4
31.660.03141.45321744.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.08 Å96.41 Å
Translation7.08 Å96.41 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7.078→96.407 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.769 / WRfactor Rfree: 0.2692 / WRfactor Rwork: 0.258 / FOM work R set: 0.7259 / SU B: 307.178 / SU ML: 2.408 / SU Rfree: 2.983 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 2.983 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3165 127 5 %RANDOM
Rwork0.2826 ---
obs0.2843 2522 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 459.21 Å2 / Biso mean: 289.798 Å2 / Biso min: 100 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 7.078→96.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3954 0 0 0 3954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194018
X-RAY DIFFRACTIONr_bond_other_d0.0020.023882
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9725458
X-RAY DIFFRACTIONr_angle_other_deg0.81538924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9275538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75125.57158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44115644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5341516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214658
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02838
X-RAY DIFFRACTIONr_mcbond_it17.42628.4672158
X-RAY DIFFRACTIONr_mcbond_other17.42428.4692157
X-RAY DIFFRACTIONr_mcangle_it30.38842.6572694
Refine LS restraints NCS

Ens-ID: 1 / Number: 15679 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 7.078→7.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.871 10 -
Rwork0.385 181 -
all-191 -
obs--95.02 %

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