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- PDB-9yfx: KrKA retaining Kdo transferase CMP complex -

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Basic information

Entry
Database: PDB / ID: 9yfx
TitleKrKA retaining Kdo transferase CMP complex
ComponentsKrKA
KeywordsTRANSFERASE / glycosyltransferase / capsule biosynthesis
Function / homologyHAD superfamily / HAD-like superfamily / metal ion binding / CYTIDINE-5'-MONOPHOSPHATE / HAD-IA family hydrolase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGovind, M. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2020-07113 Canada
CitationJournal: J.Biol.Chem. / Year: 2026
Title: The retaining Kdo transferase that synthesizes Escherichia coli K13 capsule is deeply divergent from structurally homologous enzymes.
Authors: Govind, M. / Allas, M.J. / Huang, B.S. / Lowary, T.L. / Kimber, M.S.
History
DepositionSep 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KrKA
B: KrKA
C: KrKA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6738
Polymers130,6333
Non-polymers1,0405
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-54 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.850, 132.850, 197.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein KrKA / HAD-IA family hydrolase


Mass: 43544.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AWP47_21535 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A854BIM6
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium chloride, 0.1 M glycine pH 9.5 and 20% v/v pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95358 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95358 Å / Relative weight: 1
ReflectionResolution: 2.7→46.97 Å / Num. obs: 131580 / % possible obs: 99.92 % / Redundancy: 25.2 % / Biso Wilson estimate: 82.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 6.3
Reflection shellResolution: 2.7→2.73 Å / Num. unique obs: 1094 / Rrim(I) all: 5.014

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.97 Å / SU ML: 0.3741 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2291 3790 4.1 %
Rwork0.2079 88720 -
obs0.2088 92510 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.25 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8854 0 65 63 8982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00369157
X-RAY DIFFRACTIONf_angle_d0.633512390
X-RAY DIFFRACTIONf_chiral_restr0.04491312
X-RAY DIFFRACTIONf_plane_restr0.00441546
X-RAY DIFFRACTIONf_dihedral_angle_d17.07863403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.41471390.37733234X-RAY DIFFRACTION99.85
2.73-2.770.38531370.36993322X-RAY DIFFRACTION99.74
2.77-2.810.35421420.34283274X-RAY DIFFRACTION99.82
2.81-2.850.33381390.32623276X-RAY DIFFRACTION99.85
2.85-2.890.34331400.32013278X-RAY DIFFRACTION99.91
2.89-2.940.33961410.30693308X-RAY DIFFRACTION99.86
2.94-2.980.29351430.29563246X-RAY DIFFRACTION99.82
2.98-3.040.26891420.29263304X-RAY DIFFRACTION99.83
3.04-3.090.28431370.27563287X-RAY DIFFRACTION99.88
3.09-3.150.32721420.27563278X-RAY DIFFRACTION99.97
3.15-3.210.25321410.28283292X-RAY DIFFRACTION99.97
3.21-3.280.2931440.27993288X-RAY DIFFRACTION99.94
3.28-3.360.25041380.25983302X-RAY DIFFRACTION99.94
3.36-3.440.25221360.23893266X-RAY DIFFRACTION100
3.44-3.540.24781420.23173294X-RAY DIFFRACTION99.97
3.54-3.640.28381400.22363266X-RAY DIFFRACTION99.94
3.64-3.760.22181400.21083310X-RAY DIFFRACTION100
3.76-3.890.22461400.19813313X-RAY DIFFRACTION100
3.89-4.050.18221370.19463276X-RAY DIFFRACTION100
4.05-4.230.20141460.17563274X-RAY DIFFRACTION100
4.23-4.460.19031430.16793292X-RAY DIFFRACTION100
4.46-4.740.20211350.15753306X-RAY DIFFRACTION99.94
4.74-5.10.24411430.17013280X-RAY DIFFRACTION100
5.1-5.610.20021430.19353270X-RAY DIFFRACTION99.97
5.61-6.420.23281420.2013291X-RAY DIFFRACTION100
6.42-8.090.1991350.19863300X-RAY DIFFRACTION99.91
8.09-46.970.19571430.17483293X-RAY DIFFRACTION99.94
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)
12.646763800180.75500855699-0.5243552624222.18435550523-0.9682088399231.59712890135-0.02485405456820.3798798902860.199920993162-0.4976008309430.0856495360802-0.583718576462-0.5431798962890.5726519308197.96604037665E-51.04951076238-0.2510291889790.006115647643481.461174469510.0516319633121.2580811300815.0539630071-40.5367863328-3.63149223918
20.6141913985241.047395692020.5792998558122.191964638890.3603652324361.408213052920.028732786250.136568640599-0.1536601467990.0619424242526-0.0129288016197-0.4724441763110.207432987540.1752939920531.86872098257E-50.98051351989-0.0600201272173-0.03010140817261.08366475631-0.01093268824280.9994539284042.20040194461-55.05336076186.7978443889
31.798757236530.9513890053751.18016305942.930772468781.109636077132.880657548660.01367466956290.265727243215-0.136107654381-0.3005123113550.0223770800662-0.109901398565-0.0294297212910.293558633818-2.80453679026E-50.974336970767-0.0008086684584450.03679630810121.04644095087-0.02894811953090.943491209059-7.43845477552-59.3323822269-7.23067259384
41.09330956048-0.611022384032-1.179305172923.29373958886-0.6412959655781.967362983560.004770462958230.276841686579-0.0596505343803-0.1467752564-0.07299001445330.237188878958-0.448659792655-0.0993548678031-1.29245691038E-51.12111833531-0.00701050227065-0.06478797566091.15362392843-0.05150825923380.987444802995-3.38451734666-44.324185611.5604627268
51.730780147060.7104958856680.4317720528182.978064708670.1086841836292.6673158162-0.1410580363260.53965690101-0.6043174918420.1567405623550.2304693134690.2512090019830.859749198695-0.438878081525-0.00097901160851.29565933927-0.05483223115310.08901042833490.962917832114-0.0830037611111.18610526066-29.8032324604-80.907240834919.3633542358
61.703858983970.121555178564-0.280939543221.503507405831.767293541052.41489241198-0.224084390039-0.245030531704-0.2218172960790.5246690412670.163220428137-0.06290888700820.3529956068580.147355132261-1.61809731081E-50.9837546549690.0922206923773-0.0009135329698950.9382276094490.0326797919630.922106087968-24.7503943987-64.935959009129.4776523404
75.42088687339-1.5313824927-1.273806715422.458148828041.006641767172.88110287354-0.315643576345-0.0735165726486-0.1412198599670.2370548968340.09330117535050.468392736255-0.0922615378725-0.637445779841-0.0001534556863650.8814174714160.04936410320020.006352692281061.001510256730.007468151680340.919030282637-40.6953593656-55.386577643729.5607869722
82.056488369722.39134802168-0.2783632931773.290991032580.7633942436113.06914752972-0.4142153993950.4125389844920.2387432649880.2851873139510.4927953471090.319079887604-0.312906967857-0.215368382231-0.0003379819600380.9704919633880.08369089288960.05238677607981.04313280851-0.04509272150050.853359733767-19.0496391257-58.826148999419.2103722153
91.7818809677-0.559891124305-0.8453465750141.75058882991.085725508072.28253365379-0.107415697146-0.2279994394770.4001758750070.124371612830.06491602560140.148305891989-0.594664805949-0.1357734000780.0001325810573651.192604512160.0646979706619-0.1769076865030.963365677299-0.07402961641991.14648855948-17.7048194987-23.997895796938.7845315536
102.21561358064-0.5755557495280.1706536595213.66794549401-1.828187636732.8274067008-0.1353935752140.3481265677780.5049101203130.396986872341-0.1041908166420.0955394289797-0.393769160736-0.1073945006933.47965441615E-51.13034911756-0.0923816641938-0.210265767971.014680158920.07626790310241.29323827602-9.73853949955-14.452991906115.6106479317
113.166133687680.436892227607-0.4396840461472.442044974031.734388665121.4414447607-0.2352539849310.203407159788-0.02612535931750.02788971997660.1040613468720.209031446889-0.5291635120610.05471979285544.16455910878E-50.982396096918-0.0176494064873-0.07602303465860.890196739591-0.03173675673671.03980573777-16.0790413727-38.467732434631.6693798795
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 104 )AA2 - 1041 - 103
22chain 'A' and (resid 105 through 170 )AA105 - 170104 - 169
33chain 'A' and (resid 171 through 317 )AA171 - 317170 - 314
44chain 'A' and (resid 318 through 353 )AA318 - 353315 - 350
55chain 'B' and (resid 1 through 90 )BC1 - 901 - 90
66chain 'B' and (resid 91 through 170 )BC91 - 17091 - 170
77chain 'B' and (resid 171 through 318 )BC171 - 318171 - 316
88chain 'B' and (resid 319 through 353 )BC319 - 353317 - 351
99chain 'C' and (resid 2 through 170 )CE2 - 1701 - 169
1010chain 'C' and (resid 171 through 301 )CE171 - 301170 - 298
1111chain 'C' and (resid 302 through 351 )CE302 - 351299 - 348

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