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- PDB-8prq: The structure of nvBagel2 in the presence of Cu(II) -

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Basic information

Entry
Database: PDB / ID: 8prq
TitleThe structure of nvBagel2 in the presence of Cu(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 / metal ion binding
Similarity search - Function
: / Beta-alanine-activating enzyme, beta-propeller / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamB / 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
COPPER (II) ION / Cell surface protein
Similarity search - Component
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 nvBagel2 in the presence of Cu(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)9,1783
Polymers9,0511
Non-polymers1272
Water73941
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)36,71212
Polymers36,2044
Non-polymers5088
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 area5880 Å2
ΔGint-37 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.792, 55.792, 109.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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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.) Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12) (bacteria)
Strain: ATCC 35947 / DSM 3960 / H-6-12 / Gene: DICTH_0179
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B5YBJ6
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.075 M HEPES sodium salt pH 7.5, 1.125 M Lithium sulfate, 25 %(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: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.46→49.67 Å / Num. obs: 14076 / % possible obs: 91.5 % / Redundancy: 18.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.014 / Rrim(I) all: 0.066 / Net I/σ(I): 16.6 / Num. measured all: 254799
Reflection shellResolution: 1.46→1.49 Å / % possible obs: 36 % / Redundancy: 1.8 % / Rmerge(I) obs: 1.365 / Num. measured all: 472 / Num. unique obs: 262 / CC1/2: 0.678 / Rpim(I) all: 1.138 / Rrim(I) all: 1.788 / Net I/σ(I) obs: 0.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→49.67 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2255 736 5.25 %
Rwork0.1939 --
obs0.1956 14021 91.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 2 41 655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008664
X-RAY DIFFRACTIONf_angle_d1.038907
X-RAY DIFFRACTIONf_dihedral_angle_d6.22891
X-RAY DIFFRACTIONf_chiral_restr0.09790
X-RAY DIFFRACTIONf_plane_restr0.007119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.570.35931010.34181704X-RAY DIFFRACTION60
1.57-1.730.32821520.27722744X-RAY DIFFRACTION96
1.73-1.980.26791590.18472859X-RAY DIFFRACTION99
1.98-2.50.23361590.18032907X-RAY DIFFRACTION100
2.5-49.670.19371650.18123071X-RAY DIFFRACTION100

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