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- PDB-8prr: The structure of nvBagel4 in the presence of Co(II) -

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Basic information

Entry
Database: PDB / ID: 8prr
TitleThe structure of nvBagel4 in the presence of Co(II)
ComponentsCell surface protein
KeywordsBIOSYNTHETIC PROTEIN / Protein design / symmetric / assembly / self-assembly / beta-propeller
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process
Similarity search - Function
: / PQQ-like domain / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Cell surface protein
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsVandebroek, L. / Voet, A.R.D. / Lee, X.Y.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1235722N Belgium
CitationJournal: To Be Published
Title: The structure of nvBagel4 in the presence of Co(II)
Authors: Vandebroek, L. / Voet, A.R.D. / Lee, X.Y.
History
DepositionJul 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1693
Polymers9,0511
Non-polymers1182
Water1,20767
1
A: Cell surface protein
hetero molecules

A: Cell surface protein
hetero molecules

A: Cell surface protein
hetero molecules

A: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,67512
Polymers36,2044
Non-polymers4718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area6260 Å2
ΔGint-36 kcal/mol
Surface area11730 Å2
Unit cell
Length a, b, c (Å)55.830, 55.830, 108.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-101-

CO

21A-102-

CO

31A-223-

HOH

41A-267-

HOH

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Components

#1: Protein Cell surface protein


Mass: 9050.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: DICTH_0179
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B5YBJ6
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.0085 M Cobalt chloride, 0.085 M MES pH 6.5, 1.53 M Ammonium sulfate, 15 %(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.32→54.22 Å / Num. obs: 19215 / % possible obs: 93.3 % / Redundancy: 18.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.01 / Rrim(I) all: 0.05 / Net I/σ(I): 23.6 / Num. measured all: 361486
Reflection shellResolution: 1.32→1.34 Å / % possible obs: 41.5 % / Redundancy: 2.1 % / Rmerge(I) obs: 1.646 / Num. measured all: 902 / Num. unique obs: 421 / CC1/2: 0.284 / Rpim(I) all: 1.231 / Rrim(I) all: 2.073 / Net I/σ(I) obs: 0.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→39.48 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 41.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2592 959 5 %
Rwork0.2073 --
obs0.21 19178 93.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 2 67 681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003655
X-RAY DIFFRACTIONf_angle_d0.647893
X-RAY DIFFRACTIONf_dihedral_angle_d5.889
X-RAY DIFFRACTIONf_chiral_restr0.06888
X-RAY DIFFRACTIONf_plane_restr0.005117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.390.4172950.3621599X-RAY DIFFRACTION59
1.39-1.480.43221330.32522567X-RAY DIFFRACTION94
1.48-1.590.37731470.26412741X-RAY DIFFRACTION99
1.59-1.750.25861330.20312772X-RAY DIFFRACTION100
1.75-20.23671190.1932797X-RAY DIFFRACTION100
2-2.520.24061640.19752786X-RAY DIFFRACTION100
2.53-39.480.23321680.18532957X-RAY DIFFRACTION100

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