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- PDB-8prp: The structure of nvBagel2 in the presence of Cd(II) -

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Basic information

Entry
Database: PDB / ID: 8prp
TitleThe structure of nvBagel2 in the presence of Cd(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
: / Cell surface protein
Similarity search - Component
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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 Cd(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)9,2763
Polymers9,0511
Non-polymers2252
Water362
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)37,10312
Polymers36,2044
Non-polymers8998
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 area5910 Å2
ΔGint-32 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.970, 54.970, 109.600
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-

CD

21A-102-

CD

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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 (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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.0425 M Cadmium sulfate, 0.085 M HEPES pH 7.5, 0.85 M Sodium acetate, 15 %(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.69 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.69 Å / Relative weight: 1
ReflectionResolution: 2.82→31.7 Å / Num. obs: 2236 / % possible obs: 100 % / Redundancy: 24.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.034 / Rrim(I) all: 0.166 / Net I/σ(I): 18.3 / Num. measured all: 54030
Reflection shellResolution: 2.82→2.87 Å / % possible obs: 99.1 % / Redundancy: 14.2 % / Rmerge(I) obs: 1.138 / Num. measured all: 1596 / Num. unique obs: 112 / CC1/2: 0.873 / Rpim(I) all: 0.306 / Rrim(I) all: 1.18 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia2data scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→31.7 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 19.41 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3126 116 5.19 %
Rwork0.2302 --
obs0.2346 2234 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms603 0 2 2 607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003622
X-RAY DIFFRACTIONf_angle_d0.55845
X-RAY DIFFRACTIONf_dihedral_angle_d4.74384
X-RAY DIFFRACTIONf_chiral_restr0.05185
X-RAY DIFFRACTIONf_plane_restr0.004109
LS refinement shellResolution: 2.82→31.7 Å
RfactorNum. reflection% reflection
Rfree0.3126 116 -
Rwork0.2302 2118 -
obs--100 %

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