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- PDB-9yfz: KrkA D193C ternary complex -

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Basic information

Entry
Database: PDB / ID: 9yfz
TitleKrkA D193C ternary complex
ComponentsKrKA
KeywordsTRANSFERASE / glycosyltransferase / capsule biosynthesis
Function / homologyHAD superfamily / HAD-like superfamily / metal ion binding / CYTIDINE-5'-MONOPHOSPHATE / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / HAD-IA family hydrolase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,02710
Polymers87,0652
Non-polymers1,9628
Water6,341352
1
A: KrKA
hetero molecules

A: KrKA
hetero molecules

A: KrKA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,54115
Polymers130,5973
Non-polymers2,94412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area9900 Å2
ΔGint-71 kcal/mol
Surface area43860 Å2
MethodPISA
2
B: KrKA
hetero molecules

B: KrKA
hetero molecules

B: KrKA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,54115
Polymers130,5973
Non-polymers2,94412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area9570 Å2
ΔGint-75 kcal/mol
Surface area43760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.719, 121.719, 131.962
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein KrKA / HAD-IA family hydrolase


Mass: 43532.359 Da / Num. of mol.: 2 / Mutation: D193C
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

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-ribofuranose-(1-7)-methyl 3-deoxy-beta-D-manno-oct-2-ulopyranosidonic acid


Type: oligosaccharide / Mass: 384.334 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
[][methyl]{[(1+2)][b-D-Kdop]{[(7+1)][b-D-Ribf]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O8 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 356 molecules

#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium chloride, 0.1 M HEPES pH 7.5 and 25% v/v glycerol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.21→41.18 Å / Num. obs: 55115 / % possible obs: 100 % / Redundancy: 21.5 % / Biso Wilson estimate: 26.76 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.1
Reflection shellResolution: 2.21→2.25 Å / Num. unique obs: 2735 / CC1/2: 0.312

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→41.18 Å / SU ML: 0.3102 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2532 2807 5.09 %
Rwork0.2216 52301 -
obs0.2231 55108 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.87 Å2
Refinement stepCycle: LAST / Resolution: 2.21→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 126 352 6303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236116
X-RAY DIFFRACTIONf_angle_d0.4698284
X-RAY DIFFRACTIONf_chiral_restr0.042892
X-RAY DIFFRACTIONf_plane_restr0.00341021
X-RAY DIFFRACTIONf_dihedral_angle_d12.90762244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.250.36341370.31042597X-RAY DIFFRACTION99.96
2.25-2.290.31371450.29882573X-RAY DIFFRACTION99.93
2.29-2.340.34491570.29112612X-RAY DIFFRACTION100
2.34-2.390.28031250.28862630X-RAY DIFFRACTION100
2.39-2.440.32161190.2762625X-RAY DIFFRACTION100
2.44-2.490.27461440.26962603X-RAY DIFFRACTION100
2.49-2.560.33331720.25822550X-RAY DIFFRACTION100
2.56-2.630.30421410.25562601X-RAY DIFFRACTION100
2.63-2.70.2871600.24432617X-RAY DIFFRACTION100
2.7-2.790.29121410.23712593X-RAY DIFFRACTION100
2.79-2.890.27661520.24042617X-RAY DIFFRACTION100
2.89-30.2841310.2292600X-RAY DIFFRACTION100
3.01-3.140.25011470.22742612X-RAY DIFFRACTION100
3.14-3.310.25371730.20972590X-RAY DIFFRACTION100
3.31-3.510.25311400.20792616X-RAY DIFFRACTION100
3.51-3.780.22961090.22652X-RAY DIFFRACTION100
3.79-4.170.19941110.17362646X-RAY DIFFRACTION100
4.17-4.770.18721370.1752640X-RAY DIFFRACTION100
4.77-60.20611270.19582650X-RAY DIFFRACTION100
6.01-41.180.21971390.2112677X-RAY DIFFRACTION99.93
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)
15.88557375761.347222897621.504141307741.171730591891.38755031653.026898320530.0933378496363-0.2151233904580.0739526077849-0.01596661523850.135755511218-0.301354176877-0.09940130003650.245997408314-0.2284947615450.2478841548650.07125702403490.01107255917770.204777545986-0.01366135951830.272167269325-24.8703637699-38.0844767239-14.8192144979
22.31257756914-0.881642891465-0.6147365818061.212055399540.3652684764681.259180011010.1932287353960.05770852634530.205853453023-0.286746808821-0.00416089727891-0.320729603019-0.1722516756660.269318392785-0.1643396191040.204597585295-0.03024093141360.05857348415840.182948241035-0.0233199499740.194561531799-37.1761781828-28.3289422691-20.0767526888
31.021580005670.2617248842610.06532569571152.884369657052.301868905363.042141122130.126883720394-0.0644025394690.196425461544-0.06134915836770.0230351163195-0.278483578129-0.2088573672770.210733460447-0.1388057064830.212561551461-0.0307943365250.03559504280090.203572327208-0.003865232456130.219650949407-39.7145124436-15.2343181422-5.47964700557
43.831165353210.543404966173-0.4210092313012.40392756326-0.3380076355062.277091924360.244764524114-0.112948898041-0.00856668761710.252811811304-0.2214710682760.0699906367144-0.119675196468-0.436577861325-0.003054897887120.0857328171080.0340574411745-0.04777850395890.1065654220290.0437370680760.152518804504-47.4171383107-37.1496831178-15.5042754351
53.865189679490.546079890587-0.3636855446641.23957537068-0.595689919512.680410112050.00498254786208-0.286993319434-0.5724327911710.1683709428160.2348022950060.64352998486-0.0484977268567-0.684101311587-0.1551297321580.253819295787-0.00685946273390.08043595187260.3837450114690.04577651455950.450332962862-36.9351273476-76.8610393611-31.4270827209
61.35471587208-0.128696999919-0.1197055441631.81677456855-0.5301948225240.7895205510260.03546574730770.05071016258640.03647817187360.1020111985830.04433574055690.0534765411795-0.0920622001874-0.132311103433-0.08329925189960.2106432889770.05426272455220.05937383027670.258322024405-0.02666869535050.187473073647-22.8333740962-57.2946166294-35.8714826728
75.54383248987-0.871611295195-1.412509219062.094279792590.794237832083.021452986480.025296234946-0.0744158008507-0.1161879803090.1605130211920.0875903764568-0.179625605478-0.3795200443560.115143631692-0.05164995384560.241792362455-0.01796737799960.004352667566320.140746586338-0.02213004611450.180175012655-13.1169428353-73.5193031941-31.269990612
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 81 )AA1 - 811 - 81
22chain 'A' and (resid 82 through 170 )AA82 - 17082 - 170
33chain 'A' and (resid 171 through 317 )AA171 - 317171 - 313
44chain 'A' and (resid 318 through 351 )AA318 - 351314 - 347
55chain 'B' and (resid 2 through 91 )BE2 - 911 - 90
66chain 'B' and (resid 92 through 318 )BE92 - 31891 - 311
77chain 'B' and (resid 319 through 351 )BE319 - 351312 - 344

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