PDB-9kkv: Structure-guided interface engineering for modifying substrate bi...

ID or keywords:

Entry

Database: PDB / ID: 9kkv

Title

Structure-guided interface engineering for modifying substrate binding and catalytic activity of 2-keto-3-deoxy-D-xylonate dehydratase

Components

Fumarylacetoacetate hydrolase family protein

Keywords

CARBOHYDRATE / apo

Function / homology

: / Fumarylacetoacetase-like, C-terminal domain superfamily / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / isomerase activity / hydrolase activity / DIHYDROGENPHOSPHATE ION / AMMONIUM ION / Fumarylacetoacetate hydrolase family protein

Function and homology information

Biological species

Caulobacter vibrioides NA1000 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.77 Å

Authors

Liang, B.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Structural directed engineering of 2-keto-3-deoxy-D-xylonate dehydratase for improving catalytic activity
Authors: Liang, B.

History

Deposition	Nov 14, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9kkv.cif.gz	318.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9kkv.ent.gz	257.4 KB	Display	PDB format
PDBx/mmJSON format	9kkv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kkv_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	9kkv_full_validation.pdf.gz	2.9 MB	Display
Data in XML	9kkv_validation.xml.gz	43.6 KB	Display
Data in CIF	9kkv_validation.cif.gz	63.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kk/9kkv ftp://data.pdbj.org/pub/pdb/validation_reports/kk/9kkv	HTTPS FTP

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Related structure data

Related structure data	9kktC 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	#135 - Mar 2011 Integrase similarity (1)

Deposited unit

B: Fumarylacetoacetate hydrolase family protein

A: Fumarylacetoacetate hydrolase family protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	101.808, 101.808, 211.239
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-976- HOH
2	1	A-1024- HOH

#1: Protein	Fumarylacetoacetate hydrolase family protein / 2-keto-3-deoxy-D-xylonate dehydratase apo from Caulobacter crescentus Mass: 41166.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria) Gene: xylX, CCNA_00866 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0H3C4T2, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Chemical	ChemComp-2HP / DIHYDROGENPHOSPHATE ION Mass: 96.987 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₂O₄P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H₄N / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H₂O
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: 3.32 Å³/Da / Density % sol: 63 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 1.77→50.34 Å / Num. obs: 217416 / % possible obs: 100 % / Redundancy: 3.7 % / R_merge(I) obs: 0.1 / Net I/σ(I): 101.81
Reflection shell	Resolution: 1.77→1.82 Å / Num. unique obs: 15928 / CC_1/2: 0.996

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1.5286)	refinement
PDB_EXTRACT		data extraction
HKL-3000	7.21	data scaling
PHASER	2.7.0	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.77→50.34 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.202	3801	1.84 %
R_work	0.1743	-	-
obs	0.1748	206646	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.77→50.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5731	0	23	939	6693

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006
X-RAY DIFFRACTION	f_angle_d	0.779
X-RAY DIFFRACTION	f_dihedral_angle_d	12.15	2178
X-RAY DIFFRACTION	f_chiral_restr	0.056	895
X-RAY DIFFRACTION	f_plane_restr	0.008	1069

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 (%)
1.77-1.79	0.3034	141	0.3025	7564	X-RAY DIFFRACTION	100
1.79-1.82	0.335	144	0.3206	7487	X-RAY DIFFRACTION	99
1.82-1.84	0.2868	142	0.2594	7457	X-RAY DIFFRACTION	100
1.84-1.87	0.285	144	0.2261	7504	X-RAY DIFFRACTION	100
1.87-1.9	0.2427	144	0.2094	7553	X-RAY DIFFRACTION	100
1.9-1.92	0.2568	139	0.2008	7485	X-RAY DIFFRACTION	100
1.92-1.96	0.2091	142	0.1954	7508	X-RAY DIFFRACTION	100
1.96-1.99	0.2244	139	0.1898	7490	X-RAY DIFFRACTION	100
1.99-2.03	0.2301	143	0.1881	7553	X-RAY DIFFRACTION	100
2.03-2.07	0.1916	141	0.1823	7485	X-RAY DIFFRACTION	100
2.07-2.11	0.2209	144	0.1758	7502	X-RAY DIFFRACTION	100
2.11-2.15	0.1976	135	0.1697	7556	X-RAY DIFFRACTION	100
2.15-2.2	0.2038	143	0.1729	7504	X-RAY DIFFRACTION	100
2.2-2.26	0.2071	143	0.173	7514	X-RAY DIFFRACTION	100
2.26-2.32	0.2088	143	0.1785	7513	X-RAY DIFFRACTION	100
2.32-2.39	0.221	138	0.178	7507	X-RAY DIFFRACTION	100
2.39-2.46	0.1716	141	0.1776	7497	X-RAY DIFFRACTION	100
2.46-2.55	0.1958	143	0.1729	7531	X-RAY DIFFRACTION	100
2.55-2.65	0.2441	140	0.1725	7488	X-RAY DIFFRACTION	100
2.66-2.78	0.2266	143	0.1818	7536	X-RAY DIFFRACTION	100
2.78-2.92	0.1841	136	0.1705	7497	X-RAY DIFFRACTION	100
2.92-3.11	0.1913	142	0.1688	7519	X-RAY DIFFRACTION	100
3.11-3.34	0.1893	136	0.1601	7529	X-RAY DIFFRACTION	100
3.34-3.68	0.1711	144	0.1502	7501	X-RAY DIFFRACTION	100
3.68-4.21	0.1679	134	0.143	7534	X-RAY DIFFRACTION	100
4.21-5.31	0.1549	138	0.1403	7518	X-RAY DIFFRACTION	100
5.31-50.34	0.2106	139	0.1794	7513	X-RAY DIFFRACTION	100

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	3.4719	-1.7987	0.4092	2.9806	0.7785	1.682	-0.0616	-0.2941	-0.4521	0.3267	0.0648	0.0458	0.5233	0.1362	-0.0145	0.2797	0.1119	-0.015	0.2868	0.1166	0.1905	-15.4711	14.3203	2.11
2	0.7558	0.1374	0.6663	1.2121	0.3749	1.4191	0.0025	-0.3379	-0.2441	0.3281	0.0427	-0.0388	0.3087	0.0426	-0.0443	0.2195	0.0928	0.0079	0.3057	0.0778	0.1678	-17.6486	19.3855	0.2445
3	6.6524	-1.8872	1.3884	6.9504	4.6308	8.5913	0.4292	1.0118	-1.0415	-1.0667	-0.2497	-0.5891	1.222	-0.1352	-0.2047	0.8011	0.0708	0.0029	0.444	-0.1959	0.6662	-22.1537	6.6094	-41.9558
4	4.2597	-0.1569	0.4005	1.4825	0.5813	4.9381	0.1079	0.8634	-0.7267	-0.8375	0.0092	-0.5767	0.5447	0.5843	-0.1097	0.5266	0.1024	0.1665	0.4565	-0.1272	0.4131	-17.0894	15.6131	-42.42
5	1.0322	-0.1589	0.1171	0.7623	-0.2069	1.2214	-0.0356	-0.0929	-0.2713	-0.0064	0.0304	0.0303	0.3488	-0.0079	-0.0084	0.1706	0.0236	0.027	0.1135	0.0211	0.1676	-25.6222	14.9964	-17.2531
6	3.7907	0.0426	-2.1733	0.0003	-0.0275	1.9617	-0.1625	-0.0487	-0.6254	-0.2069	-0.2043	-0.2433	0.4958	-0.0313	0.3312	0.2526	0.0496	0.0146	0.2004	-0.0282	0.2376	-16.6383	12.487	-22.9626
7	2.11	0.3839	0.1795	2.9432	0.0914	1.7838	-0.0496	0.0781	-0.4243	-0.1467	0.0462	0.0035	0.4166	-0.1524	0.0129	0.1531	0.0129	0.0253	0.1792	-0.0058	0.164	-24.4682	16.7518	-20.2257
8	1.6168	0.2793	0.2722	1.9875	0.5182	1.1274	-0.0256	-0.1656	-0.2174	0.1633	-0.0293	0.0806	0.3037	-0.0656	0.0464	0.1833	0.0208	0.0397	0.1673	0.0878	0.1158	-29.862	15.7846	-5.2096
9	6.5269	-2.429	-0.2484	3.0722	0.0741	1.8325	0.1094	0.2206	0.3427	-0.083	-0.0998	0.04	-0.475	-0.0845	-0.0239	0.1863	0.0654	0.0264	0.1645	-0.0448	0.1265	-35.8786	54.3798	-9.9804
10	0.4549	0.1609	-0.0266	1.2612	0.9523	2.1337	-0.0135	-0.08	0.0841	0.0255	0.0784	-0.0064	-0.1288	0.0183	-0.0617	0.0609	0.0312	0.0186	0.1209	-0.0096	0.1142	-34.2542	45.4632	-14.9052
11	3.91	2.8243	-0.5592	2.5997	-0.8003	0.3604	-0.1435	0.2277	0.0016	-0.27	0.2031	0.1704	0.1518	-0.2199	-0.0576	0.1539	-0.0372	-0.0301	0.1825	0.0069	0.1578	-47.8622	26.676	-40.0498
12	0.5732	0.1016	0.114	0.6001	0.0332	0.9915	-0.0462	-0.0199	0.0094	-0.0255	0.0474	0.0307	-0.028	-0.0696	-0.0026	0.0663	0.009	0.013	0.1124	-0.0067	0.0845	-34.7439	39.6691	-23.8031

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 2 through 32 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 33 through 104 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 105 through 135 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 136 through 159 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 160 through 282 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 283 through 304 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 305 through 333 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 334 through 384 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 2 through 32 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 33 through 120 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 121 through 158 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 159 through 384 )

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