PDB-9yfy: KrkA D193C Kdo adduct

ID or keywords:

Entry

Database: PDB / ID: 9yfy

Title

KrkA D193C Kdo adduct

Components

KrKA

Keywords

TRANSFERASE / glycosyltransferase

Function / homology

HAD superfamily / HAD-like superfamily / metal ion binding / CYTIDINE-5'-MONOPHOSPHATE / GLYCINE / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / HAD-IA family hydrolase

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 Å

Authors

Govind, M. / Kimber, M.S.

Funding support

Canada, 1items

Citation

Journal: 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

Deposition	Sep 27, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 28, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9yfy.cif.gz	531.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9yfy.ent.gz	368.1 KB	Display	PDB format
PDBx/mmJSON format	9yfy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yf/9yfy ftp://data.pdbj.org/pub/pdb/validation_reports/yf/9yfy	HTTPS FTP

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Related structure data

Related structure data	9yfxC 9yfzC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: KrKA

B: KrKA

hetero molecules

88.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: KrKA

hetero molecules

A: KrKA

hetero molecules

A: KrKA

hetero molecules

defined by author&software
133 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: KrKA

hetero molecules

B: KrKA

hetero molecules

B: KrKA

hetero molecules

defined by author&software
133 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.150, 121.150, 131.496
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃
Space group name Hall	P6c
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

ID	Model	Components
1	1	A-630- HOH

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Protein / Sugars , 2 types, 4 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
Details: residues C-terminal to 354 are deleted / Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: NCTC9022 / Gene: AWP47_21535 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A854BIM6

#3: 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

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Non-polymers , 4 types, 264 molecules

#2: 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
#4: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 61.56 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 10, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9201 Å / Relative weight: 1
Reflection	Resolution: 2.027→40.44 Å / Num. obs: 70912 / % possible obs: 100 % / Redundancy: 21.3 % / B_iso Wilson estimate: 25.66 Å² / CC_1/2: 0.996 / Net I/σ(I): 11.1
Reflection shell	Resolution: 2.03→2.03 Å / Num. unique obs: 3520 / CC_1/2: 0.367

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.03→40.44 Å / SU ML: 0.2687 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.251	3608	5.09 %
R_work	0.2224	67299	-
obs	0.2239	70907	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 34.69 Å²

Refinement step

Cycle: LAST / Resolution: 2.03→40.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5881	0	86	256	6223

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6158
X-RAY DIFFRACTION	f_angle_d	0.4891	8337
X-RAY DIFFRACTION	f_chiral_restr	0.0448	885
X-RAY DIFFRACTION	f_plane_restr	0.0034	1038
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9219	2231

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.03-2.05	0.3544	135	0.309	2601	X-RAY DIFFRACTION	100
2.05-2.08	0.3159	142	0.3016	2546	X-RAY DIFFRACTION	100
2.08-2.11	0.3047	144	0.2966	2556	X-RAY DIFFRACTION	100
2.11-2.14	0.3319	168	0.2856	2550	X-RAY DIFFRACTION	100
2.14-2.18	0.3297	117	0.2853	2619	X-RAY DIFFRACTION	100
2.18-2.21	0.2819	119	0.2702	2626	X-RAY DIFFRACTION	100
2.21-2.25	0.3205	135	0.2616	2554	X-RAY DIFFRACTION	100
2.25-2.29	0.2929	158	0.2644	2583	X-RAY DIFFRACTION	100
2.29-2.33	0.2829	146	0.2508	2559	X-RAY DIFFRACTION	100
2.33-2.38	0.3013	138	0.2522	2598	X-RAY DIFFRACTION	100
2.38-2.43	0.2608	141	0.2373	2545	X-RAY DIFFRACTION	100
2.43-2.49	0.2688	154	0.2377	2578	X-RAY DIFFRACTION	100
2.49-2.55	0.2606	113	0.2419	2617	X-RAY DIFFRACTION	100
2.55-2.62	0.2492	145	0.2311	2585	X-RAY DIFFRACTION	100
2.62-2.7	0.2645	173	0.2304	2550	X-RAY DIFFRACTION	100
2.7-2.79	0.2341	141	0.2291	2574	X-RAY DIFFRACTION	100
2.79-2.89	0.2691	114	0.2322	2645	X-RAY DIFFRACTION	100
2.89-3	0.2643	127	0.2228	2563	X-RAY DIFFRACTION	100
3-3.14	0.2826	143	0.234	2601	X-RAY DIFFRACTION	100
3.14-3.3	0.2507	115	0.2185	2613	X-RAY DIFFRACTION	100
3.3-3.51	0.2563	119	0.2144	2596	X-RAY DIFFRACTION	100
3.51-3.78	0.2239	149	0.198	2592	X-RAY DIFFRACTION	100
3.78-4.16	0.2147	122	0.1786	2621	X-RAY DIFFRACTION	100
4.16-4.76	0.2107	142	0.178	2588	X-RAY DIFFRACTION	100
4.76-6	0.2099	137	0.1942	2628	X-RAY DIFFRACTION	100
6-40.44	0.2075	171	0.2057	2611	X-RAY DIFFRACTION	99.86

Refinement TLS params.

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

ID	L11 (°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)
1	2.06949885063	-0.300738665835	0.269179319552	1.61666324489	0.232065047374	1.01827161513	0.109944303485	-0.0633880621517	-0.466306261263	0.00276053564904	0.063574960488	-0.129381329694	0.215864168464	0.0756781901688	-0.137913170409	0.184803148634	0.0198852265279	-0.0464400744858	0.18301671771	0.0191846414836	0.227611829537	16.182	41.489	26.523
2	4.95038601672	-0.594411295669	1.04840986003	4.21786814502	1.58167206507	1.27386534782	-0.0549237848025	0.0501711916565	0.101683143502	-0.41843077072	-0.117621577581	0.105537692145	-0.256324379574	-0.27586322354	0.220665404206	0.173029011715	-0.0295366191379	0.0402828546101	0.167002109994	0.0645174940829	0.0773235091909	-15.083	53.913	14.797
3	2.35940841666	0.80998386683	2.10854106511	1.30040949321	1.10172155075	2.81117255106	0.143007417258	-0.0245846742396	-0.395021548543	-0.0279128683097	0.0429640315693	0.0248521446689	0.250818255433	-0.0677729180476	-0.164572943625	0.1795728034	-0.00932931422276	-0.0189353590749	0.161952539704	0.0328154199644	0.229838287933	-5.224	41.436	14.601
4	1.04652810048	0.585363407956	0.00405456545348	3.43921742948	0.377030051427	2.56883984835	-0.10837472028	-0.034382575555	0.136369487815	-0.356109467227	0.109919461868	0.160207544602	-0.446579277761	-0.0985621581229	0.0859636635509	0.0403660771089	0.0544639346075	0.0529417312335	0.178208636387	-0.0145543502384	0.172585200011	6.975	57.431	21.688
5	1.08348798077	-0.698648999493	-0.373551344535	3.4842796308	0.198718877229	2.33564095972	0.243813260778	0.283331960204	0.958541103645	-0.00219151620559	0.0233286581062	-0.167070523688	-0.599452036356	-0.269369312673	-0.169519856287	0.326112608519	0.0621202487038	0.0419973442159	0.294790151546	0.133623213498	0.538999449042	47.852	69.688	38.667
6	1.66659917662	0.111890329919	-0.200922540884	3.99891857789	-1.63425232175	1.49055288746	-0.0406097531668	0.249586211066	0.167707670684	-0.166637941616	0.1221994844	0.191290610874	-0.055066929702	-0.168705391211	-0.0840304773244	0.137568006093	0.0149014275166	-0.0493444485416	0.228069506331	0.0190513974671	0.173727321199	44.216	48.215	35.582
7	3.38725255533	0.388048018545	-1.79828981661	1.77504103224	-0.851572161886	2.16444582674	-0.0298887501749	-0.171606557615	-0.0022456724161	0.146689678413	0.162873645229	0.0768830476667	-0.0221875971058	-0.0703434209009	-0.123634243661	0.145641583253	0.0395209805884	-0.0792912776584	0.234114235673	0.0392924993373	0.183238178457	34.216	46.18	49.311
8	4.85141871149	-0.489774292037	-0.466135959802	1.65179434035	0.56589074416	0.230743668817	0.199277597849	-0.242132226982	-0.232791895418	-0.137637264516	-0.0844619142206	-0.140477357342	0.0210889242031	0.0732242682956	-0.0117063002683	0.227443719633	0.00972189930423	0.0102672231862	0.133657006809	-0.0192039243445	0.196190286586	54.062	47.033	42.166

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:153 )	A	1 - 153
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 154:187 )	A	154 - 187
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 188:318 )	A	188 - 318
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 319:352 )	A	319 - 352
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 2:104 )	B	2 - 104
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 105:170 )	B	105 - 170
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 171:318 )	B	171 - 318
8	X-RAY DIFFRACTION	8	( CHAIN B AND ( RESID 319:354 OR RESID 401:403 ) )	B	319 - 354
9	X-RAY DIFFRACTION	8	( CHAIN B AND ( RESID 319:354 OR RESID 401:403 ) )	B	401 - 403

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