PDB-4fjs: Crystal structure of ureidoglycolate dehydrogenase enzyme in apo form

ID or keywords:

Entry

Database: PDB / ID: 4fjs

Title

Crystal structure of ureidoglycolate dehydrogenase enzyme in apo form

Components

Ureidoglycolate dehydrogenase

Keywords

OXIDOREDUCTASE / ALLD / NAD(P)H-DEPENDENT OXIDOREDUCTASE / UREIDE PATHWAY / UREIDOGLYCOLATE / OXALURATE / ANTIPARALLEL BETA-SHEET FOLD / UREIDOGLYCOLATE DEHYDROGENASE

Function / homology

Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta / :

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.13 Å

Authors

Kim, M.I. / Shin, I. / Lee, J. / Rhee, S.

Citation

Journal: Plos One / Year: 2012
Title: Structural and functional insights into (s)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization.
Authors: Kim, M.I. / Shin, I. / Cho, S. / Lee, J. / Rhee, S.

History

Deposition	Jun 12, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 16, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Jul 17, 2019	Group: Data collection / Refinement description / Category: software Item: _software.classification / _software.name / _software.version
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fjs.cif.gz	146.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4fjs.ent.gz	115.9 KB	Display	PDB format
PDBx/mmJSON format	4fjs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fjs_validation.pdf.gz	434.8 KB	Display	wwPDB validaton report
Full document	4fjs_full_validation.pdf.gz	450.7 KB	Display
Data in XML	4fjs_validation.xml.gz	30.9 KB	Display
Data in CIF	4fjs_validation.cif.gz	45.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fj/4fjs ftp://data.pdbj.org/pub/pdb/validation_reports/fj/4fjs	HTTPS FTP

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Related structure data

Related structure data	4fjuC 4h8aC 1xhrS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4h8a-d 1xrh-4 1nxu-d 1xrh-3 1vbi-1 4faa-d 5luz-2 4g7s-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ureidoglycolate dehydrogenase

B: Ureidoglycolate dehydrogenase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	162.760, 162.760, 61.450
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-460- HOH
2	1	B-403- HOH
3	1	B-556- HOH

#1: Protein	Ureidoglycolate dehydrogenase Mass: 38201.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH10B / Gene: allD, b0517, ECDH10B_0473, glxB8, JW0505, ylbC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1XGB5, EC: 1.1.1.154
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Ureidoglycolate dehydrogenase

Mass: 38201.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: DH10B / Gene: allD, b0517, ECDH10B_0473, glxB8, JW0505, ylbC / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1XGB5, EC: 1.1.1.154

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.37 %
Crystal grow	Method: evaporation / pH: 6 / Details: 0.1M MES, 4.0M NACL, pH 6.0, EVAPORATION

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2010
Radiation	Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. obs: 46352 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 23.2 % / R_merge(I) obs: 0.123 / Net I/σ(I): 6.7
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 16.9 % / R_merge(I) obs: 0.606 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.7.2_869	refinement
CNS		refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1XHR

1xhr

Resolution: 2.13→49.18 Å / SU ML: 0.5 / σ(F): 1.34 / Phase error: 24.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.24	2000	4.32 %
R_work	0.222	-	-
obs	0.223	46305	99 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 34.58 Å² / k_sol: 0.35 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.321 Å²	0 Å²	-0 Å²
2-	-	1.321 Å²	-0 Å²
3-	-	-	-2.6419 Å²

Refinement step

Cycle: LAST / Resolution: 2.13→49.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4959	0	0	500	5459

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5065
X-RAY DIFFRACTION	f_angle_d	1.113	6865
X-RAY DIFFRACTION	f_dihedral_angle_d	17.15	1843
X-RAY DIFFRACTION	f_chiral_restr	0.079	750
X-RAY DIFFRACTION	f_plane_restr	0.005	913

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 (%)
2.1301-2.1834	0.289	133	0.2835	2949	X-RAY DIFFRACTION	94
2.1834-2.2425	0.2959	138	0.2696	3042	X-RAY DIFFRACTION	97
2.2425-2.3084	0.2821	139	0.268	3089	X-RAY DIFFRACTION	98
2.3084-2.3829	0.2661	141	0.2609	3128	X-RAY DIFFRACTION	99
2.3829-2.4681	0.376	141	0.2633	3128	X-RAY DIFFRACTION	100
2.4681-2.5669	0.3014	142	0.2727	3150	X-RAY DIFFRACTION	100
2.5669-2.6837	0.3114	143	0.2621	3158	X-RAY DIFFRACTION	100
2.6837-2.8252	0.2697	142	0.2503	3155	X-RAY DIFFRACTION	100
2.8252-3.0022	0.2804	143	0.2385	3178	X-RAY DIFFRACTION	100
3.0022-3.234	0.2096	145	0.2345	3189	X-RAY DIFFRACTION	100
3.234-3.5593	0.214	144	0.2	3205	X-RAY DIFFRACTION	100
3.5593-4.0742	0.1825	147	0.1745	3233	X-RAY DIFFRACTION	100
4.0742-5.1321	0.1786	148	0.1692	3272	X-RAY DIFFRACTION	100
5.1321-49.194	0.2371	154	0.2167	3429	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	0.0085	-0.0058	-0.0046	0.0145	-0.0123	0.0199	0.0165	0.0383	-0.0276	0.004	0.0291	-0.0072	0.0263	0.0327	0.0335	0.3997	0.3023	-0.0463	0.7394	-0.1958	0.3541	64.6459	-30.6321	-21.4922
2	0.0102	0.0021	-0.0172	0.0146	0.014	0.0769	-0.0244	0.0561	-0.0179	0.083	0.1476	-0.0137	0.0753	0.1978	0.0882	0.1659	0.134	-0.0246	0.4477	-0.116	0.2604	59.8816	-24.9866	-16.7384
3	0.0613	-0.0463	0.03	0.0716	-0.0373	0.1444	0.0284	0.0105	-0.1408	0.0854	0.1112	0.0391	0.2421	0.0487	0.0948	0.2354	0.1108	-0.0812	0.1514	-0.0097	0.2519	44.2296	-32.3199	-10.0572
4	0.01	-0.0137	0.025	0.0197	-0.0302	0.051	0.0049	0.0173	-0.0321	0.0416	0.0281	-0.0733	0.0551	0.0829	-0.0763	0.1088	0.0402	-0.0243	0.1633	-0.0361	0.1841	45.997	-17.6586	-12.7895
5	0.0299	-0.0316	0.0054	0.0281	0.0069	0.0162	0.0413	0.0882	0.0099	-0.05	-0.0408	-0.0737	-0.0599	0.1295	-0.0277	0.1845	-0.0927	0.0131	0.3008	-0.0241	0.2719	57.388	-5.2354	-15.447
6	0.0423	-0.0421	0.0108	0.1229	-0.0586	0.0346	-0.0291	-0.0712	-0.0337	0.0084	0.1136	0.0226	-0.059	0.1218	0.0077	0.158	-0.0161	-0.0212	0.1792	-0.0277	0.1656	48.1475	-6.1953	-7.4633
7	0.1225	-0.1331	-0.0585	0.2261	0.121	0.1431	-0.0987	0.0857	-0.0525	-0.0096	0.1653	-0.0139	-0.0207	0.2097	-0.0366	0.096	-0.0769	-0.0114	0.2051	-0.0327	0.1332	45.2532	-16.1859	-22.3429
8	0.0067	-0.0075	-0.0038	0.0011	-0.0002	0.0046	-0.0762	0.0186	0.0079	-0.0371	0.0646	-0.0481	-0.0256	0.067	-0	0.3374	0.1837	-0.0045	0.9233	-0.1722	0.3435	71.4347	-24.0172	-20.045
9	0.0628	-0.0062	0.0106	0.0642	-0.0202	0.0078	-0.0145	-0.0439	0.0081	0.0549	0.0261	0.0113	-0.0573	-0.0907	0.1172	0.3372	0.5379	-0.1162	0.4264	-0.2256	0.2957	12.1137	2.9836	-8.8961
10	0.0014	0.0018	-0.0031	0.0071	-0.0107	0.0161	0.0285	0.0285	0.033	-0.0346	0.02	0.0565	-0.0526	-0.0136	0.0423	0.4847	0.2579	-0.267	0.2256	-0.1098	0.445	19.25	6.422	-16.7797
11	0.0741	-0.0295	-0.0439	0.0558	0.02	0.0301	-0.0553	-0.0133	-0.0099	-0.0029	-0.132	0.0442	-0.0489	-0.1943	-0.1413	0.147	0.0494	-0.06	0.2275	-0.0321	0.1943	14.2264	-13.411	-21.5453
12	0.0294	-0.018	-0.0258	0.0222	0.0363	0.083	-0.0751	-0.1499	0.0157	-0.0382	-0.0307	0.0492	0.001	-0.2171	-0.0823	0.1263	0.0524	-0.0138	0.1895	-0.0068	0.1476	21.7581	-12.5393	-11.7932
13	0.4749	0.0363	0.0245	0.1036	0.0551	0.0302	-0.1092	-0.156	0.0868	-0.0874	0.0232	0.0558	-0.1435	0.0605	-0.0452	0.1573	0.005	-0.0192	0.1241	0.0152	0.1444	33.2663	-5.6097	-15.4703
14	0.0135	-0.0062	0.0152	0.0132	-0.0174	0.0302	-0.015	-0.0461	0.0147	0.0237	-0.0454	0.0492	-0.0664	-0.02	-0.016	0.3516	-0.075	-0.0543	0.0997	-0.0391	0.2949	36.3173	13.1522	-20.6414
15	0.0361	-0.0237	-0.0307	0.0387	0.0196	0.0304	-0.1228	0.0533	0.0381	-0.0556	0.0186	0.0974	-0.1598	0.0715	-0.0863	0.2261	-0.0669	-0.0692	0.1024	0.0121	0.1604	39.4722	2.6311	-26.5852
16	0.0834	0.0667	-0.1213	0.055	-0.1001	0.1794	-0.0978	0.0501	0.0042	-0.0884	-0.0293	-0.026	-0.0926	0.0089	-0.0762	0.1743	0.0094	-0.0896	0.0869	0.0167	0.1785	23.4283	-3.8764	-29.9964
17	0.1268	0.0437	-0.0253	0.0306	-0.0097	0.0938	0.0314	-0.1802	-0.0006	0.0442	0.0318	0.0822	-0.0026	-0.0124	0.0633	0.1164	0.0091	-0.0081	0.1882	0.0082	0.1083	34.1803	-15.1208	-0.8702
18	0.0029	-0.0041	-0.0003	0.0159	-0.0134	0.0132	-0.0188	-0.0631	0.0555	0.048	-0.036	0.0106	-0.0858	-0.1146	-0.0093	0.2466	0.0448	-0.0731	0.2874	-0.0802	0.2427	38.0446	3.7978	1.3185

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:22)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 23:57)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 58:104)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 105:164)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 165:211)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 212:236)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 237:319)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 320:337)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 3:38)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 39:57)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 58:85)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 86:129)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 130:175)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 176:200)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 201:236)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 237:260)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 261:291)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 292:317)

Xplor file

Refine-ID	Serial no	Param file
X-RAY DIFFRACTION	1	PROTEIN_REP.PARAM
X-RAY DIFFRACTION	2	DNA-RNA_REP.PARAM
X-RAY DIFFRACTION	3	WATER_REP.PARAM
X-RAY DIFFRACTION	4	ION.PARAM
X-RAY DIFFRACTION	5	CARBOHYDRATE.PARAM

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