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- PDB-7zyb: BeKdgF with Ca -

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Basic information

Entry
Database: PDB / ID: 7zyb
TitleBeKdgF with Ca
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: 1.5 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)15,1664
Polymers14,9941
Non-polymers1723
Water1,11762
1
A: Cupin
hetero molecules

A: Cupin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3338
Polymers29,9882
Non-polymers3446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area3720 Å2
ΔGint-54 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.374, 47.374, 175.859
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-202-

CA

21A-360-

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 (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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 80mM MES pH 6.5, 14.4% (w/v) PEG8000, 20% v/v glycerol, 160mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→41.03 Å / Num. obs: 19628 / % possible obs: 98.85 % / Redundancy: 13.3 % / Biso Wilson estimate: 25.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05293 / Rpim(I) all: 0.01441 / Rrim(I) all: 0.05497 / Net I/σ(I): 20.91
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 4.8 % / Rmerge(I) obs: 2.167 / Mean I/σ(I) obs: 0.62 / Num. unique obs: 1845 / CC1/2: 0.808 / Rpim(I) all: 1.069 / Rrim(I) all: 2.431 / % possible all: 95.32

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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: 1.5→41.03 Å / SU ML: 0.1686 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6828
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2008 953 4.87 %
Rwork0.173 18626 -
obs0.1744 19579 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.88 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 8 62 951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022960
X-RAY DIFFRACTIONf_angle_d1.78621300
X-RAY DIFFRACTIONf_chiral_restr0.1342140
X-RAY DIFFRACTIONf_plane_restr0.0108171
X-RAY DIFFRACTIONf_dihedral_angle_d18.0947354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.43331320.3912481X-RAY DIFFRACTION94.57
1.58-1.680.28071360.26172556X-RAY DIFFRACTION98.32
1.68-1.80.25921200.19542630X-RAY DIFFRACTION99.46
1.81-1.990.19971450.15832628X-RAY DIFFRACTION99.07
1.99-2.270.19191190.16132677X-RAY DIFFRACTION99.29
2.27-2.860.22111460.19352705X-RAY DIFFRACTION99.76
2.87-41.030.17731550.15432949X-RAY DIFFRACTION99.84
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)
10.256098581274-0.0397956759416-0.06101518831320.2016111402880.02979052893010.4643253064020.136569178237-0.0559063282297-0.4854426944610.391202846487-0.2092140510.3067687238641.22757152795-0.8423920794980.01365126183640.542903256251-0.0834643764622-0.03204330751660.399981297232-0.1173727226570.44244845241918.4366754402-13.73620840176.296258108
20.0358603529074-0.04547953092390.01463364493530.127444435160.03590369285330.0483386811339-0.07893737908330.38741673175-0.676417799597-0.2711492352730.1188760188890.5512822190160.651037581623-0.1604924541280.002790970839180.550844808044-0.0811839414737-0.03806643924790.756146348536-0.1495100186440.54384606123412.4717014693-10.551242275565.4770405904
30.1232361070790.07943426181470.1243309579610.2123857930250.07664210361090.123311484120.3144038914630.514124357841-0.544726473414-0.1324312841070.1372887162280.9958379645620.00428438849922-1.1999815445-0.01083958429960.3246468745060.074250126144-0.05603037429930.7204126545640.04115184686080.4835161992667.89218074582-0.9851844977968.5580200509
40.5934496990720.226981843039-0.3375953166470.748167537473-0.008261599191270.2038485686810.05575888154330.3312586324480.0433085439729-0.147191116178-0.01035974013690.06642012849890.207111764669-0.70019506185-0.0001604117684260.2578406232550.0163554040795-0.01232733173230.369643771433-0.004763320535050.30944621572917.0210176278-2.8591595485574.4242558699
50.453048548789-0.1992362271991.144324235830.287723190323-0.7842685740653.21574102770.06136100171950.2988856092290.3285312737880.02208106481740.06302660759320.252080210185-1.33942738669-1.146002433390.04583680300180.4394318039370.1987513516010.01628100592760.7161261506850.05413939959370.44444351161710.38961400049.4759435963871.893850412
60.4136223764420.3770596827790.08197802361430.3447687519210.03342767637420.1811828973150.1329640346410.3246382847110.270095929112-0.123938926177-0.03629413886880.138612730065-1.02031134477-0.1422261437040.0004734550723550.434973838930.1504165568860.01858936104040.3973233370970.0718574072870.3348360784619.52496559539.5929425729668.5283587073
70.07663572528670.0927763656434-0.008656950200920.1430530908420.04984579437550.06277892505740.0324627656684-0.06402556526970.8719669098330.1651001664170.173584339621-0.434814268357-0.7340151923890.54773203296-0.0006734901152490.7473269636380.1045683160670.01797260122220.478375764770.1241428402640.52076243520620.61580475917.93523508168.6622521514
80.579553799544-0.01308501754-0.2366062595050.545412673017-0.4551240030280.4884041968030.105652113110.3171658264670.2465373532890.0142827982021-0.1495394787590.0487541358917-0.613723672957-0.363346919186-0.0001510990720710.3255228365280.1098019522490.01110932032810.3573816753670.05395790364190.32245111800718.45424862968.8826852224671.1950300115
90.5709607275250.09505353345830.1156848615120.1893816398240.2842641751891.558868366870.01174282341560.0250613517461-0.7045008799430.501172417580.2239411897540.7007763576190.485768874502-1.420154993910.005429796279220.285305144599-0.02042413333260.03435502735970.5343916100850.01867265369030.47840151693111.148180564-1.8180696543181.637556358
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 2 through 10 )2 - 101 - 9
22chain 'A' and (resid 11 through 16 )11 - 1610 - 15
33chain 'A' and (resid 17 through 27 )17 - 2716 - 28
44chain 'A' and (resid 28 through 41 )28 - 4129 - 42
55chain 'A' and (resid 42 through 54 )42 - 5443 - 57
66chain 'A' and (resid 55 through 69 )55 - 6958 - 72
77chain 'A' and (resid 70 through 77 )70 - 7773 - 80
88chain 'A' and (resid 78 through 105 )78 - 10581 - 110
99chain 'A' and (resid 106 through 113 )106 - 113111 - 118

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