PDB-5ti1: Crystal Structure of Fumarylacetoacetate hydrolase from Burkholde...

ID or keywords:

Entry

Database: PDB / ID: 5ti1

Title

Crystal Structure of Fumarylacetoacetate hydrolase from Burkholderia xenovorans LB400

Components

Fumarylacetoacetate hydrolase

Keywords

HYDROLASE / fumarylacetoacetate hydrolase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

fumarylacetoacetase / fumarylacetoacetase activity / homogentisate catabolic process / tyrosine catabolic process / L-phenylalanine catabolic process / metal ion binding
Similarity search - Function

Biological species

Burkholderia xenovorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / SSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal Structure of Fumarylacetoacetate hydrolase from Burkholderia xenovorans LB400
Authors: Seattle Structural Genomics Center for Infectious Disease / Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E.

History

Deposition	Sep 30, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 2, 2017	Group: Other / Structure summary Category: audit_author / pdbx_database_status / struct_keywords Item: _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ti1.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb5ti1.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	5ti1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ti1_validation.pdf.gz	497.7 KB	Display	wwPDB validaton report
Full document	5ti1_full_validation.pdf.gz	510 KB	Display
Data in XML	5ti1_validation.xml.gz	139.3 KB	Display
Data in CIF	5ti1_validation.cif.gz	203 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ti/5ti1 ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5ti1	HTTPS FTP

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Related structure data

Related structure data	4qkuS S: Starting model for refinement
Similar structure data	4qku-1 4kfn-d 4qku-2 2wx5-d 3vh3-1 1foe-3 1foe-4 4o15-d 2bnp-d 1pj5-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4qkuS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fumarylacetoacetate hydrolase

B: Fumarylacetoacetate hydrolase

C: Fumarylacetoacetate hydrolase

D: Fumarylacetoacetate hydrolase

E: Fumarylacetoacetate hydrolase

F: Fumarylacetoacetate hydrolase

G: Fumarylacetoacetate hydrolase

H: Fumarylacetoacetate hydrolase

hetero molecules

389 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fumarylacetoacetate hydrolase

B: Fumarylacetoacetate hydrolase

hetero molecules

defined by author&software
97.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Fumarylacetoacetate hydrolase

D: Fumarylacetoacetate hydrolase

hetero molecules

defined by author&software
97.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Fumarylacetoacetate hydrolase

F: Fumarylacetoacetate hydrolase

hetero molecules

defined by author&software
97.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Fumarylacetoacetate hydrolase

H: Fumarylacetoacetate hydrolase

hetero molecules

defined by author&software
97.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.900, 83.100, 186.290
Angle α, β, γ (deg.)	101.63, 91.17, 113.81
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Fumarylacetoacetate hydrolase Mass: 48518.301 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria) Strain: LB400 / Gene: Bxe_A3899 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q144Z1, fumarylacetoacetase

#1: Protein

Fumarylacetoacetate hydrolase

Mass: 48518.301 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_A3899 / Cell line (production host): BL21(DE3) / Production host:

Escherichia coli (E. coli) / References: UniProt: Q144Z1, fumarylacetoacetase

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Non-polymers , 5 types, 2668 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO₃
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2644 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.49 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: tray272143 Morpheus C1: 10%Peg 20K, 20%Peg MME 550, 0.03 M NPS, 0.1M MES/imidazole, pH 6.5; cryo: direct; BuxeA.00077.d.B1.PS37875 at 22.1 mg/ml, puck jua8-10

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 227227 / % possible obs: 95.6 % / Redundancy: 1.99 % / R_merge(I) obs: 0.053 / R_sym value: 0.075 / Net I/σ(I): 12.81
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 1.99 % / R_merge(I) obs: 0.378 / R_sym value: 0.535 / % possible all: 94.8

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2499: ???)	refinement
HKL-2000		data collection
XDS		data scaling
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4qku

4qku

Resolution: 2→40.311 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1988	2001	0.88 %
R_work	0.1543	-	-
obs	0.1547	227167	95.55 %

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→40.311 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26062	0	49	2644	28755

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	27084
X-RAY DIFFRACTION	f_angle_d	0.821	36985
X-RAY DIFFRACTION	f_dihedral_angle_d	13.483	16128
X-RAY DIFFRACTION	f_chiral_restr	0.052	4123
X-RAY DIFFRACTION	f_plane_restr	0.006	4924

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 (%)
1.9999-2.0499	0.2731	131	0.2396	15927	X-RAY DIFFRACTION	95
2.0499-2.1053	0.2769	142	0.226	15967	X-RAY DIFFRACTION	95
2.1053-2.1673	0.2876	154	0.2092	16001	X-RAY DIFFRACTION	95
2.1673-2.2372	0.2585	151	0.1927	16037	X-RAY DIFFRACTION	95
2.2372-2.3172	0.2414	123	0.1778	16001	X-RAY DIFFRACTION	95
2.3172-2.4099	0.2037	124	0.1696	16021	X-RAY DIFFRACTION	95
2.4099-2.5196	0.2007	152	0.1648	16143	X-RAY DIFFRACTION	95
2.5196-2.6524	0.2274	169	0.1652	16072	X-RAY DIFFRACTION	96
2.6524-2.8186	0.2067	142	0.1643	16049	X-RAY DIFFRACTION	96
2.8186-3.0361	0.2042	151	0.1616	16161	X-RAY DIFFRACTION	96
3.0361-3.3415	0.2048	146	0.1573	16130	X-RAY DIFFRACTION	96
3.3415-3.8247	0.1829	145	0.1369	16216	X-RAY DIFFRACTION	96
3.8247-4.8175	0.1445	144	0.1098	16335	X-RAY DIFFRACTION	97
4.8175-40.3191	0.1509	127	0.1268	16106	X-RAY DIFFRACTION	96

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	0.7195	0.1347	0.1375	1.7174	-0.8204	2.5358	0.1416	-0.2751	0.0821	0.7032	-0.2711	-0.2929	-0.9659	0.756	-0.0423	0.6397	-0.2166	-0.0656	0.4383	-0.0112	0.215	22.2384	38.025	2.6685
2	0.3669	0.2393	-0.4206	1.1207	-1.0659	2.3767	0.0744	0.0136	0.131	0.2777	0.2412	0.2938	-0.3085	-0.6256	-0.1669	0.2964	0.0913	0.0792	0.3448	0.0558	0.2267	-1.9803	27.3222	-0.2583
3	1.2022	-0.1994	-0.5117	0.7869	-0.6632	1.8057	0.2637	0.0982	0.2026	0.2685	0.2344	0.2744	-0.6905	-0.9531	-0.1357	0.4465	0.1987	0.1654	0.4186	0.1375	0.3145	-2.774	37.8036	-12.1739
4	0.7642	0.0584	0.1532	1.0603	-0.9434	2.3832	-0.1276	0.139	-0.0217	-0.3584	-0.1529	-0.2412	1.0204	0.4058	-0.0016	0.8238	0.1868	0.1606	0.2848	0.0002	0.1917	21.1771	-6.8557	-3.3323
5	0.3594	0.2277	-0.0445	0.952	-0.8093	1.8199	-0.0729	0.069	-0.0326	-0.2589	0.1965	0.1117	0.7937	-0.4918	-0.0449	0.5729	-0.1519	-0.024	0.3336	0.0143	0.1797	-0.9121	-0.3961	0.2114
6	1.2366	0.3176	0.0637	1.5658	0.1958	1.8472	-0.0531	-0.1163	0.3254	0.2053	-0.1156	0.4137	-0.8501	-0.2617	0.1518	0.8077	0.1003	0.0101	0.2391	-0.0457	0.3147	3.6988	30.7245	48.6905
7	0.4845	-0.0363	-0.0212	0.7915	-0.5298	1.7355	-0.024	-0.0483	0.162	0.2479	-0.1205	-0.1338	-0.6516	0.4184	0.1167	0.537	-0.1407	-0.0359	0.2607	0.0093	0.2378	23.6281	18.9607	50.4012
8	1.7352	0.4669	0.1575	0.9745	-0.4224	1.3474	0.0231	-0.0298	-0.1208	-0.1666	0.0811	0.1708	0.4184	-0.3124	-0.088	0.4959	-0.1115	-0.0275	0.263	0.0144	0.1671	-2.9111	-12.9879	39.3406
9	0.4515	0.0237	-0.0257	0.6909	-0.4449	1.8796	-0.0014	0.0269	-0.0487	-0.1265	-0.0773	-0.1149	0.4267	0.2842	0.0806	0.3976	0.0466	0.0314	0.2058	0.0153	0.1774	19.7435	-7.6458	38.1719
10	1.6804	0.6796	0.0018	1.4364	-0.3178	1.7927	-0.0747	0.0323	0.0807	0.0111	0.0002	-0.2438	-0.5212	0.2315	0.0457	0.2987	-0.0611	-0.0135	0.1568	-0.015	0.1917	24.5368	8.0173	91.467
11	0.5131	0.0766	-0.0109	1.0885	-0.4057	1.3203	-0.039	-0.0152	0.0841	-0.0406	0.0817	0.1393	-0.3996	-0.3191	-0.0192	0.2062	0.0745	0.0065	0.1903	-0.0168	0.1743	2.5516	0.7757	87.2787
12	2.2494	-0.526	-0.0155	1.7303	-0.0928	1.1947	-0.0019	0.079	-0.2428	-0.2403	-0.0104	-0.3361	0.2929	0.1395	-0.0199	0.2561	0.0127	0.0537	0.1493	-0.0241	0.2314	24.2343	-36.4138	85.7858
13	0.3586	0.0387	0.2208	1.1522	-0.0841	1.3674	-0.0123	0.0283	-0.0665	-0.1883	0.0517	0.1599	0.2369	-0.2737	-0.0064	0.1563	-0.0449	-0.01	0.1844	-0.0151	0.1884	2.5501	-26.6998	87.2324
14	2.2365	-0.4546	-0.8416	1.7014	0.3338	1.5771	0.0547	-0.0398	-0.2147	-0.011	-0.0652	0.2037	0.4722	-0.3986	0.0541	0.2173	-0.0937	-0.0224	0.2151	0.0239	0.2106	1.3906	-37.2699	98.984
15	1.7577	-0.1434	0.1907	1.5979	0.3025	0.9767	-0.0656	-0.0935	0.2265	-0.1868	-0.0644	0.4877	-0.3771	-0.1989	0.0441	0.3285	0.1006	-0.0541	0.1814	-0.0523	0.2979	-4.3252	15.1113	138.5441
16	0.4422	0.1049	-0.0489	0.9228	0.0037	1.2222	-0.0177	-0.0968	0.1203	0.1043	0.007	-0.0755	-0.3699	0.1548	0.0087	0.2289	-0.0046	-0.0157	0.1648	-0.0421	0.1902	16.5705	6.3037	143.7381
17	2.2327	0.9084	0.7211	1.3652	0.1508	1.8498	0.0255	-0.0595	-0.1774	0.0351	0.0326	0.2202	0.2557	-0.292	-0.0521	0.1518	-0.0018	0.018	0.1714	-0.0029	0.1941	-3.9456	-29.7281	131.2335
18	0.2699	0.1618	-0.0096	0.9414	-0.1634	1.2615	-0.0283	-0.0565	-0.0241	0.0379	0.0454	-0.147	-0.0145	0.2323	0.0053	0.1018	0.0322	0.0028	0.1579	-0.0316	0.1716	17.6258	-15.8326	133.186
19	0.2996	-0.0195	0.0309	0.7	0.1251	1.7686	-0.002	-0.0046	-0.1409	-0.0153	0.0325	-0.0898	0.311	0.2632	-0.0126	0.1466	0.0609	-0.0228	0.1645	-0.0228	0.2106	18.2303	-26.4556	131.6265

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 4:149 )	A	4 - 149
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 150:374 )	A	150 - 374
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 375:436 )	A	375 - 436
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 4:160 )	B	4 - 160
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 161:436 )	B	161 - 436
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID 5:160 )	C	5 - 160
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 161:436 )	C	161 - 436
8	X-RAY DIFFRACTION	8	( CHAIN D AND RESID 4:160 )	D	4 - 160
9	X-RAY DIFFRACTION	9	( CHAIN D AND RESID 161:436 )	D	161 - 436
10	X-RAY DIFFRACTION	10	( CHAIN E AND RESID 3:160 )	E	3 - 160
11	X-RAY DIFFRACTION	11	( CHAIN E AND RESID 161:436 )	E	161 - 436
12	X-RAY DIFFRACTION	12	( CHAIN F AND RESID 4:160 )	F	4 - 160
13	X-RAY DIFFRACTION	13	( CHAIN F AND RESID 161:374 )	F	161 - 374
14	X-RAY DIFFRACTION	14	( CHAIN F AND RESID 375:436 )	F	375 - 436
15	X-RAY DIFFRACTION	15	( CHAIN G AND RESID 3:160 )	G	3 - 160
16	X-RAY DIFFRACTION	16	( CHAIN G AND RESID 161:436 )	G	161 - 436
17	X-RAY DIFFRACTION	17	( CHAIN H AND RESID 3:160 )	H	3 - 160
18	X-RAY DIFFRACTION	18	( CHAIN H AND RESID 161:291 )	H	161 - 291
19	X-RAY DIFFRACTION	19	( CHAIN H AND RESID 292:436 )	H	292 - 436

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Yorodumi