PDB-4n04: The crystal structure of glyoxalase / bleomycin resistance protei...

ID or keywords:

Entry

Database: PDB / ID: 4n04

Title

The crystal structure of glyoxalase / bleomycin resistance protein from Catenulispora Acidiphila DSM 44928

Components

Glyoxalase/bleomycin resistance protein/dioxygenase

Keywords

OXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / TRANSPORT PROTEIN / ALPHA/BETA FOLD / ANTIBIOTIC INHIBITOR PROTEIN / CYTOPLASMIC

Function / homology

Function and homology information

dioxygenase activity
Similarity search - Function

Biological species

Catenulispora acidiphila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.489 Å

Authors

Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The crystal structure of glyoxalase / bleomycin resistance protein from catenulispora acidiphila dsm 44928
Authors: Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Sep 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4n04.cif.gz	101.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4n04.ent.gz	81 KB	Display	PDB format
PDBx/mmJSON format	4n04.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/n0/4n04 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n04	HTTPS FTP

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Related structure data

Similar structure data	3e9v-d 3d7b-1 1o0o-1 5f71-2 5e5f-1 5jml-1 3dxh-1 3dju-d 5ubd-2 5jmg-1 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
Other databases	TargetTrack: MCSG-APC103217

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glyoxalase/bleomycin resistance protein/dioxygenase

B: Glyoxalase/bleomycin resistance protein/dioxygenase

hetero molecules

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

1

A: Glyoxalase/bleomycin resistance protein/dioxygenase

hetero molecules

defined by author
12.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glyoxalase/bleomycin resistance protein/dioxygenase

hetero molecules

defined by author
13.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	123.600, 123.600, 123.600
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	199
Space group name H-M	I2₁3

#1: Protein	Glyoxalase/bleomycin resistance protein/dioxygenase Mass: 12714.806 Da / Num. of mol.: 2 / Mutation: V61M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Catenulispora acidiphila (bacteria) / Strain: DSM 44928 / Gene: Caci_7252 / Plasmid: PMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: C7Q893
#2: Chemical	ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₇NO₃S / Comment: pH buffer*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.09 Å³/Da / Density % sol: 60.24 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1 M CHES:NaOH pH 9.5 1.0 M Sodium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012 / Details: MIRRORS
Radiation	Monochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97899 Å / Relative weight: 1
Reflection	Resolution: 2.48→50 Å / Num. obs: 11068 / % possible obs: 99 % / Redundancy: 18.7 % / R_sym value: 0.057 / Net I/σ(I): 21.5
Reflection shell	Resolution: 2.48→2.52 Å / Redundancy: 19.2 % / Mean I/σ(I) obs: 6.6 / R_sym value: 0.674 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
MLPHARE		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.489→39.086 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 22.85 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2274	525	4.74 %
R_work	0.1763	-	-
obs	0.1786	11068	98.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.489→39.086 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1695	0	38	42	1775

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1769
X-RAY DIFFRACTION	f_angle_d	1.198	2403
X-RAY DIFFRACTION	f_dihedral_angle_d	16.294	621
X-RAY DIFFRACTION	f_chiral_restr	0.079	261
X-RAY DIFFRACTION	f_plane_restr	0.005	311

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 (%)
2.489-2.7394	0.3504	133	0.232	2637	X-RAY DIFFRACTION	100
2.7394-3.1357	0.2529	133	0.2048	2626	X-RAY DIFFRACTION	100
3.1357-3.95	0.2184	136	0.1611	2649	X-RAY DIFFRACTION	100
3.95-39.0906	0.1745	123	0.151	2631	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	3.342	0.0293	-0.6684	4.6768	-1.7434	2.4648	-0.1875	0.1634	0.3679	-0.0388	-0.0697	-0.1375	-0.4789	-0.007	0.0189	0.4299	-0.003	-0.1926	0.1683	0.1345	0.5136	70.8278	48.7566	38.1417
2	0.8829	-0.3143	0.1613	0.4275	0.0899	0.1862	-0.0641	-0.0157	0.3544	0.113	-0.0088	0.065	-0.3498	-0.0736	0.0489	0.7917	0.4525	-0.2985	-0.1246	-0.0086	0.6778	65.4749	55.4186	48.7327
3	0.7652	0.627	0.472	2.8809	-0.7137	1.5545	-0.1447	0.0279	0.2313	-0.0351	0.0306	0.192	-0.1945	-0.1432	0.006	0.8886	0.186	-0.4492	0.0822	0.2249	0.7605	65.1686	58.8158	38.8648
4	4.043	-4.2723	1.1878	5.993	-3.3121	3.2168	0.014	0.0454	0.1766	0.1209	0.0334	-0.2274	-0.2207	0.0629	0.1194	0.7339	-0.0121	-0.3428	0.1028	0.1489	0.57	72.3815	55.9799	39.9769
5	1.757	2.2593	0.6482	5.9349	0.1972	1.8587	-0.2411	0.0384	0.3335	-0.011	0.0635	-0.1268	-0.49	0.0156	0.1165	0.5215	0.0077	-0.1811	0.1802	0.0492	0.5794	71.553	51.7295	38.8885
6	3.5106	-0.2404	-2.3233	1.9893	0.8651	1.7902	-0.1237	0.4238	0.3491	-0.2732	0.0076	0.3971	-0.4477	-0.4678	0.0985	0.3208	0.0728	-0.1084	0.3108	0.0509	0.526	60.9078	41.4076	42.6105
7	3.9421	0.0341	0.4603	7.6319	4.5537	5.8538	-0.218	-0.4138	0.6024	0.8356	0.0528	-0.6622	-0.6783	0.3204	0.0579	0.8062	-0.0629	-0.3368	0.2635	0.1233	0.6788	78.5212	52.3297	53.1773
8	0.8589	-1.3896	-0.1376	2.2751	0.2336	0.0261	0.0701	0.2792	0.2409	0.0199	-0.1971	0.1741	-0.6994	-0.0546	0.1707	0.9352	0.1427	-0.2821	0.3362	-0.0488	0.6	70.2142	54.1373	58.5605
9	2.3619	0.2121	-3.1573	1.801	0.1257	4.3247	-0.1636	0.0856	-0.0784	-0.1423	-0.111	-0.4667	-0.0625	0.5051	0.1812	0.5437	0.081	-0.1587	0.5628	0.0424	0.544	83.3499	42.282	60.1477
10	8.871	-0.9846	2.8521	3.8151	0.0172	4.9372	-0.1683	-0.0664	-0.027	0.5845	-0.0998	-0.3352	-0.1929	0.1476	0.17	0.4537	0.0666	-0.1614	0.2349	0.0352	0.3846	71.1523	46.2073	54.1019
11	3.3328	-3.2949	-1.7249	3.5943	0.7524	3.5677	-0.109	-0.761	0.7389	0.6117	0.0088	-0.749	-0.1794	0.6348	0.2287	0.5643	-0.0242	-0.2941	0.3889	0.0638	0.6434	80.1197	46.8751	52.33
12	0.6493	-0.3013	-0.8273	2.4608	0.3385	2.6831	-0.0401	0.204	0.2333	0.0342	-0.1576	-0.3227	-0.0828	0.4945	0.1102	0.2747	0.0112	-0.1084	0.1827	0.1137	0.3859	77.4301	35.1017	38.2211
13	1.7775	0.4258	0.4592	0.3851	-0.7965	3.0922	0.1088	0.1369	0.0005	-0.1072	-0.0806	-0.3264	0.5203	0.4863	0.0937	0.2568	0.0782	-0.0629	0.3494	0.1283	0.3821	84.5998	31.6121	41.6473
14	7.4809	0.0438	3.2054	7.4827	-0.4979	8.9062	0.0089	0.4452	0.5357	-0.0385	-0.0763	-0.5716	-0.3513	0.7477	0.1159	0.1656	0.0283	-0.0272	0.2915	0.104	0.5134	83.5337	38.7724	38.4379
15	5.1229	4.7491	-3.1744	7.9198	-4.0484	2.5329	-0.0842	0.0542	0.1798	0.1833	-0.1057	-0.6962	-0.2516	0.5584	0.1975	0.2615	-0.0657	-0.0705	0.2661	0.1152	0.3982	80.1615	40.0075	41.0384
16	4.4007	0.5147	-1.6893	8.2225	2.6595	1.6513	-0.2015	-0.1893	0.0979	0.5176	-0.036	0.0018	0.0302	-0.0865	0.1383	0.1795	0.0473	-0.021	0.2079	0.0727	0.3444	66.9096	34.2611	45.6739
17	3.9279	-0.6671	-1.9619	1.5186	0.6667	3.2441	-0.1144	0.1891	0.3315	-0.3657	-0.0513	-0.4293	-0.6066	0.2062	0.135	0.4857	0.0052	-0.0067	0.2222	0.128	0.5669	74.7594	45.899	30.2292
18	4.2477	-1.8964	2.085	4.5023	1.2588	2.3368	0.0249	0.6947	0.2219	-1.1788	0.008	-0.1443	0.0691	0.2175	-0.0547	0.5273	0.1178	0.0639	0.286	0.0911	0.3067	75.8138	35.3646	21.9858
19	3.1256	1.1193	0.0849	3.8382	-5.0743	7.5827	0.1408	0.1025	0.3498	-0.0589	0.0396	0.1312	-0.3062	-0.1577	-0.1198	0.6228	0.1086	-0.0149	0.392	0.1988	0.4369	65.6669	48.1775	20.6654
20	0.9978	0.2153	-0.2319	3.885	-2.9968	5.6505	0.1644	0.349	0.2061	-0.1835	-0.0628	-0.059	-0.2332	-0.1676	-0.0113	0.3293	0.0528	-0.1284	0.2768	0.1491	0.3738	68.6344	37.6386	30.0189
21	2.9683	-2.5397	1.5694	8.0458	1.845	2.56	-0.0635	0.6071	0.374	-0.6458	-0.1625	-0.8246	-0.338	0.0987	0.2732	0.3753	0.0366	-0.0763	0.2894	0.1416	0.457	72.0251	44.5338	28.067

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 25 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 26 through 36 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 37 through 43 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 44 through 52 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 53 through 60 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 61 through 78 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 79 through 84 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 85 through 93 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 94 through 104 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 105 through 112 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 2 through 25 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 26 through 36 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 37 through 43 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 44 through 52 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 53 through 60 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 61 through 68 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 69 through 84 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 85 through 93 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 94 through 104 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 105 through 111 )

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