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

ID or keywords:

Entry

Database: PDB / ID: 9kkt

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 / 2-OXO-4-METHYLPENTANOIC ACID / Fumarylacetoacetate hydrolase family protein

Function and homology information

Biological species

Caulobacter vibrioides NA1000 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 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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PDBx/mmCIF format	9kkt.cif.gz	313.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9kkt.ent.gz	253.1 KB	Display	PDB format
PDBx/mmJSON format	9kkt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kkt_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	9kkt_full_validation.pdf.gz	2 MB	Display
Data in XML	9kkt_validation.xml.gz	40.5 KB	Display
Data in CIF	9kkt_validation.cif.gz	57 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kk/9kkt ftp://data.pdbj.org/pub/pdb/validation_reports/kk/9kkt	HTTPS FTP

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Related structure data

Related structure data	9kkvC 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

Deposited unit

B: Fumarylacetoacetate hydrolase family protein

A: Fumarylacetoacetate hydrolase family protein

hetero molecules

82.6 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)	102.160, 102.160, 211.770
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-836- HOH

#1: Protein	Fumarylacetoacetate hydrolase family protein / 2-keto-3-deoxy-D-xylonate dehydratase 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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical	ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 634 / 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: 3.38 Å³/Da / Density % sol: 63.63 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium malonate dialkali monohydrate, 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.01→31.06 Å / Num. obs: 75354 / % possible obs: 100 % / Redundancy: 3.7 % / R_merge(I) obs: 0.085 / Net I/σ(I): 102.16
Reflection shell	Resolution: 2.01→2.06 Å / Num. unique obs: 5470 / CC_1/2: 0.995

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.01→31.06 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2076	3695	4.91 %
R_work	0.1751	-	-
obs	0.1767	75242	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.01→31.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5722	0	19	634	6375

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5850
X-RAY DIFFRACTION	f_angle_d	0.816	7939
X-RAY DIFFRACTION	f_dihedral_angle_d	13.355	3506
X-RAY DIFFRACTION	f_chiral_restr	0.054	886
X-RAY DIFFRACTION	f_plane_restr	0.005	1057

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 (%)
2.01-2.0365	0.3045	158	0.2622	2693	X-RAY DIFFRACTION	100
2.0365-2.0643	0.2746	140	0.2501	2702	X-RAY DIFFRACTION	100
2.0643-2.0938	0.2752	137	0.234	2708	X-RAY DIFFRACTION	100
2.0938-2.1251	0.2803	140	0.2133	2716	X-RAY DIFFRACTION	100
2.1251-2.1583	0.259	127	0.2116	2712	X-RAY DIFFRACTION	100
2.1583-2.1936	0.2547	134	0.2043	2727	X-RAY DIFFRACTION	100
2.1936-2.2315	0.2396	133	0.1969	2703	X-RAY DIFFRACTION	100
2.2315-2.272	0.2269	152	0.1909	2723	X-RAY DIFFRACTION	100
2.272-2.3157	0.2381	130	0.1862	2720	X-RAY DIFFRACTION	100
2.3157-2.363	0.2416	145	0.185	2705	X-RAY DIFFRACTION	100
2.363-2.4143	0.2753	142	0.19	2732	X-RAY DIFFRACTION	100
2.4143-2.4704	0.2543	135	0.1902	2731	X-RAY DIFFRACTION	100
2.4704-2.5322	0.2353	135	0.1866	2736	X-RAY DIFFRACTION	100
2.5322-2.6006	0.2214	123	0.1747	2739	X-RAY DIFFRACTION	100
2.6006-2.6771	0.2129	131	0.1891	2771	X-RAY DIFFRACTION	100
2.6771-2.7635	0.2423	143	0.1918	2733	X-RAY DIFFRACTION	100
2.7635-2.8621	0.2443	167	0.183	2707	X-RAY DIFFRACTION	100
2.8621-2.9766	0.2171	138	0.187	2746	X-RAY DIFFRACTION	100
2.9766-3.112	0.219	156	0.1857	2747	X-RAY DIFFRACTION	100
3.112-3.2759	0.2294	142	0.1877	2766	X-RAY DIFFRACTION	100
3.2759-3.4808	0.1973	135	0.1794	2767	X-RAY DIFFRACTION	100
3.4808-3.7491	0.1957	160	0.167	2776	X-RAY DIFFRACTION	100
3.7491-4.1255	0.1928	150	0.1546	2798	X-RAY DIFFRACTION	100
4.1255-4.7204	0.1593	156	0.1356	2806	X-RAY DIFFRACTION	100
4.7204-5.9396	0.1641	151	0.1471	2853	X-RAY DIFFRACTION	100
5.9396-29.8401	0.1681	135	0.1707	3030	X-RAY DIFFRACTION	99

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	3.4569	-0.3616	0.206	3.7455	0.7721	2.612	0.066	-0.4055	0.3809	0.2351	0.0063	0.1612	-0.4824	-0.345	-0.0615	0.3782	0.0914	0.0727	0.4234	-0.0838	0.2817	-38.2219	31.5962	2.3437
2	2.1755	0.5745	-0.7594	2.8748	1.0013	4.7734	0.0963	-0.4545	0.374	0.4989	-0.0454	0.0222	-0.4822	0.1034	-0.0146	0.3734	0.0583	-0.0291	0.2894	-0.0838	0.3192	-26.0786	36.6009	-2.2039
3	6.524	1.2057	-1.0475	2.2858	-2.2735	6.8921	0.665	1.1956	0.8988	-0.8942	0.234	1.6375	-0.8269	-0.4299	-0.8127	1.0897	0.2133	-0.1532	0.6106	0.1785	1.0518	-28.8291	44.5045	-41.8896
4	9.3897	-0.2218	-1.5171	4.7076	-1.3547	2.3018	0.0678	1.0739	0.9681	-1.3732	0.1916	1.1334	-0.7867	-1.0464	-0.2591	0.8508	0.0858	-0.2685	0.6022	0.1061	0.6251	-34.3643	35.4637	-42.0558
5	1.6609	-0.0503	-0.2384	1.1658	0.0635	1.641	-0.0295	-0.0899	0.3701	-0.0169	-0.0029	0.0224	-0.47	0.064	0.034	0.3556	0.0025	-0.0522	0.1994	-0.0328	0.3151	-25.2739	36.0499	-17.6202
6	5.4499	-0.045	1.9401	0.1305	-0.1079	1.2596	-0.1808	0.027	0.9292	-0.1854	-0.1746	0.3574	-0.6395	0.0337	0.3566	0.4801	0.0432	-0.026	0.2875	0.0162	0.3886	-34.2856	38.9347	-22.9528
7	2.4573	0.7651	0.4699	2.2212	-0.2806	1.6521	-0.1232	-0.022	0.4084	0.1236	0.0328	0.0929	-0.4993	0.1249	0.0795	0.3204	0.0223	-0.0125	0.2414	-0.0539	0.2399	-22.9944	34.8775	-10.9446
8	7.3431	-2.4439	-1.6495	5.7932	0.6965	4.2882	0.2463	0.2616	-0.307	-0.0715	-0.1643	-0.2296	0.6315	0.1326	-0.0736	0.2905	0.0844	-0.0575	0.2305	0.0362	0.2047	-15.0361	-3.3799	-10.1209
9	0.3327	0.563	-0.0111	7.2168	1.0024	2.1232	0.1123	-0.1468	-0.0921	0.3094	-0.1534	-0.3014	0.0282	0.0186	0.0471	0.2703	0.0266	-0.0736	0.3523	0.0419	0.2589	-12.8019	1.7813	-0.4038
10	2.0857	2.0072	-1.0583	4.5476	-1.2029	3.1171	-0.0384	-0.0416	-0.1292	0.0532	0.0205	0.2169	0.369	-0.2514	0.0324	0.1795	0.031	-0.0602	0.2865	0.0363	0.254	-21.5769	1.4187	-16.3496
11	4.4635	-2.0812	1.4339	4.1161	2.2066	5.0185	-0.002	0.4496	0.2389	-0.4721	0.0172	-0.1715	-0.6374	0.2804	-0.0331	0.3648	-0.0818	0.0158	0.312	0.049	0.2633	-13.0556	19.9854	-43.6159
12	4.7007	-4.2356	-1.1752	8.5663	-3.4473	9.0166	-0.1276	0.0039	0.0101	-0.3116	0.1458	-0.3303	-0.2522	0.4332	-0.0765	0.2058	-0.1099	0.0341	0.2817	0.0197	0.3325	1.9767	27.1361	-35.4446
13	0.662	0.0842	-0.0478	0.8271	-0.3006	1.4842	-0.0514	-0.018	-0.0127	0.0143	0.0213	-0.0812	-0.0203	0.0684	0.0329	0.1684	-0.0017	-0.0236	0.2204	0.0103	0.2181	-16.1588	11.2586	-23.8922

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 3 through 67 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 68 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 158 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 159 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 384 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 3 through 32 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 33 through 67 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 68 through 104 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 105 through 134 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 135 through 158 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 159 through 384 )

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