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- PDB-7zyc: BeKdgF with Zn -

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Basic information

Entry
Database: PDB / ID: 7zyc
TitleBeKdgF with Zn
ComponentsCupin
KeywordsHYDROLASE / enzyme
Function / homologyPectin degradation protein KdgF / : / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Cupin
Function and homology information
Biological speciesBacteroides eggerthii DSM 20697 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFredslund, F. / Teze, D. / Welner, D.H.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20CC0035580 Denmark
Danish Agency for Science Technology and Innovation7129-00003B Denmark
CitationJournal: To Be Published
Title: BeKdgF with Ca
Authors: Fredslund, F. / Teze, D. / Welner, D.H.
History
DepositionMay 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cupin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2174
Polymers14,9941
Non-polymers2233
Water1448
1
A: Cupin
hetero molecules

A: Cupin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4348
Polymers29,9882
Non-polymers4466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area3800 Å2
ΔGint-104 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.660, 46.660, 176.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-203-

ZN

21A-308-

HOH

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Components

#1: Protein Cupin / Cupin domain-containing protein


Mass: 14994.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii DSM 20697 (bacteria)
Gene: DW701_08695, DWZ51_01720, EAJ03_07795, NCTC11155_02558
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A380Z821
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.85 Å3/Da / Density % sol: 33.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 200mM potassium formate, 20% (w/v) PEG3500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→40.41 Å / Num. obs: 14428 / % possible obs: 98.85 % / Redundancy: 19.8 % / Biso Wilson estimate: 42.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08276 / Rpim(I) all: 0.01915 / Rrim(I) all: 0.08506 / Net I/σ(I): 23.56
Reflection shellResolution: 2→2.072 Å / Redundancy: 15.7 % / Rmerge(I) obs: 1.549 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 799 / CC1/2: 0.921 / Rpim(I) all: 0.3952 / Rrim(I) all: 1.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fpx

5fpx


Resolution: 2→40.41 Å / SU ML: 0.2872 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.9758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2597 1440 9.98 %
Rwork0.2279 12988 -
obs0.2312 14428 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.96 Å2
Refinement stepCycle: LAST / Resolution: 2→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 0 8 8 888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095895
X-RAY DIFFRACTIONf_angle_d0.8641203
X-RAY DIFFRACTIONf_chiral_restr0.059130
X-RAY DIFFRACTIONf_plane_restr0.0051155
X-RAY DIFFRACTIONf_dihedral_angle_d16.488323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.54361350.46391241X-RAY DIFFRACTION95.22
2.07-2.150.42791460.4141297X-RAY DIFFRACTION98.3
2.15-2.250.39721460.36731301X-RAY DIFFRACTION98.5
2.25-2.370.34161480.33471296X-RAY DIFFRACTION98.63
2.37-2.520.39471420.30271296X-RAY DIFFRACTION98.29
2.52-2.710.36021430.30071297X-RAY DIFFRACTION98.63
2.71-2.980.25381420.24041304X-RAY DIFFRACTION99.25
2.98-3.420.29171550.22251301X-RAY DIFFRACTION99.59
3.42-4.30.20951390.18081331X-RAY DIFFRACTION99.66
4.31-40.410.19071440.18081324X-RAY DIFFRACTION99.86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3479580132350.3886200765210.04388631274120.4302217338370.1606260584970.1142663927540.0513199851126-0.0252085096183-0.302510187336-0.01149719902670.3403350579350.4351786322470.342651941858-0.521836983916-0.0002886599250570.632035669013-0.0693909287567-0.09205280608670.7063747495930.03091104777340.66477743485413.418979318-6.8749876759372.1823306088
2-0.00166826263079-0.00824521996109-0.0004256700370260.0178768604256-0.00160945346140.004191037971160.7601973866930.1350182936930.464949087941-0.5763678095330.1362527183150.920072597726-0.294126201575-0.174425891066-5.03485862522E-50.587082630992-0.053267018976-0.08218830884570.6632340996390.05012504636020.66139230823714.7301357507-0.074857386481469.7549219668
30.08937245134080.3307388706390.4416285579820.73395275561-0.1721405317550.5118420524040.01056368112260.2203222277610.0835221914269-0.002459929531110.06714055179530.261369018675-0.530884496682-0.59749391505-2.00069635959E-50.6569764316740.112071759780.02271873078170.6078353020310.05405817564760.59429303149816.25779177648.8607073162272.7801307334
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 34 )3 - 341 - 32
22chain 'A' and (resid 35 through 41 )35 - 4133 - 39
33chain 'A' and (resid 42 through 113 )42 - 11340 - 111

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