PDB-4gym: Crystal structure of Glyoxalase/bleomycin resistance protein/diox...

ID or keywords:

Entry

Database: PDB / ID: 4gym

Title

Crystal structure of Glyoxalase/bleomycin resistance protein/dioxygenase from Conexibacter woesei DSM 14684

Components

Glyoxalase/bleomycin resistance protein/dioxygenase

Keywords

OXIDOREDUCTASE / PSI-Biology / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG

Function / homology

Function and homology information

dioxygenase activity
Similarity search - Function

Biological species

Conexibacter woesei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.56 Å

Authors

Chang, C. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of Glyoxalase/bleomycin resistance protein/dioxygenase from Conexibacter woesei DSM 14684
Authors: Chang, C. / Tesar, C. / Clancy, S. / Joachimiak, A.

History

Deposition	Sep 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4gym.cif.gz	133.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4gym.ent.gz	113.9 KB	Display	PDB format
PDBx/mmJSON format	4gym.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/gy/4gym ftp://data.pdbj.org/pub/pdb/validation_reports/gy/4gym	HTTPS FTP

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Related structure data

Similar structure data	5mm6-d 5ahg-d 6k34-4 2owp-d 3dnm-1 5cxx-3 4u0p-d 4ue7-d 3b9h-d 6s0v-4 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: APC103354

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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

33.2 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)	58.943, 58.943, 164.990
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Glyoxalase/bleomycin resistance protein/dioxygenase Mass: 16510.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Conexibacter woesei (bacteria) / Strain: DSM 14684 / Gene: Cwoe_2487 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D3F7P7
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.17 Å³/Da / Density % sol: 43.32 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M MgCl2, 0.1M This-Cl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 17, 2012
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 1.56→50 Å / Num. all: 42532 / Num. obs: 41562 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / R_merge(I) obs: 0.115 / Net I/σ(I): 24.9
Reflection shell	Resolution: 1.56→1.57 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.939 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1044 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.11	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
DM		phasing
SHELXDE		phasing
ARP/wARP		model building
RESOLVE		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.56→37.2 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.958 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.753 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1869	2075	5 %	RANDOM
R_work	0.1543	-	-	-
all	0.156	41178	-	-
obs	0.156	41178	96.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 81.52 Å² / B_iso mean: 16.9125 Å² / B_iso min: 6.37 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	0 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	0.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→37.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2154	0	10	219	2383

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	2354
X-RAY DIFFRACTION	r_angle_refined_deg	1.362	1.936	3209
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.767	5	312
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.318	24.074	108
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.187	15	370
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.625	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	349
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1854
X-RAY DIFFRACTION	r_rigid_bond_restr	2.541	3	2354
X-RAY DIFFRACTION	r_sphericity_free	24.996	5	61
X-RAY DIFFRACTION	r_sphericity_bonded	10.863	5	2452

LS refinement shell

Resolution: 1.56→1.6 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.26	154	-
R_work	0.213	2550	-
all	-	2704	-
obs	-	2704	96.09 %

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	2.2638	-0.9004	-0.3412	1.753	-0.8373	0.7303	-0.0686	-0.1512	0.1145	0.1897	0.0599	-0.0844	-0.1041	0.0224	0.0087	0.033	-0.0002	-0.0076	0.0155	-0.0062	0.0235	30.4386	6.2427	62.9482
2	0.2339	-0.1233	0.0091	0.0747	-0.0442	0.1629	0.0101	0.0019	0.0037	-0.0066	-0.0017	0.0005	0.0021	-0.0022	-0.0083	0.0185	-0.0006	-0.0014	0.0147	-0.0005	0.0179	19.8921	7.4103	45.8782
3	0.4815	0.2709	-0.2031	1.1182	0.8942	1.1582	0.0315	-0.0014	0.0341	-0.0516	0.025	-0.0277	-0.0623	0.0195	-0.0565	0.034	-0.0075	0.0102	0.0131	0.0039	0.018	26.785	16.0033	48.3629
4	0.0789	-0.1989	0.0792	0.5486	0.2004	3.4617	0.0009	0.0128	0.0254	-0.0124	-0.0163	-0.0649	-0.0823	0.1549	0.0155	0.0178	-0.0047	0.001	0.0205	-0.0013	0.0225	23.5336	9.1603	55.8165
5	0.3853	-0.4188	-0.1751	0.6036	-0.0159	0.3661	-0.001	-0.022	0.0183	0.0188	0.0054	-0.0237	-0.0275	0.0339	-0.0044	0.0207	-0.0031	0.0033	0.0188	0.0006	0.0073	32.8689	5.232	42.2793
6	0.2804	0.1076	-0.0413	0.0865	0.0656	0.1612	-0.0089	0.0148	0.0016	-0.0086	0.0059	0.0018	0.0049	-0.0047	0.003	0.0229	0.0003	-0.0003	0.0155	-0.0015	0.0128	32.3301	-4.6017	44.2983
7	0.4445	0.0474	-0.0385	0.263	0.0569	0.0179	-0.0012	-0.0315	-0.0089	0.021	-0.0006	0.0088	0.0051	0.0043	0.0018	0.0182	-0.0011	-0.0014	0.0184	0.0012	0.0196	11.5149	-3.8562	52.9397
8	5.4818	5.1659	-3.9253	5.1638	-5.6187	15.2857	0.1638	-0.0741	-0.1612	0.1709	-0.1426	-0.1318	-0.1667	0.4769	-0.0212	0.0605	-0.0173	-0.0025	0.0194	-0.0049	0.0127	8.9915	-4.6341	70.4571
9	11.1438	-3.5104	3.9749	7.6291	-1.868	3.8639	0.1315	0.1486	-0.029	-0.2236	-0.1358	0.2767	0.0487	-0.0237	0.0043	0.0272	-0.0101	-0.008	0.0171	-0.0055	0.0117	25.8942	-5.141	75.3505
10	1.9556	-0.7687	-0.5986	3.1016	2.0757	1.6772	-0.0073	0.05	0.0886	-0.1417	0.0322	0.0216	-0.0929	0.0076	-0.0249	0.0092	0.0039	-0.0043	0.0291	-0.0005	0.0136	12.902	16.2449	61.6151
11	0.1119	-0.0578	0.033	0.0704	-0.0607	0.06	-0.0015	-0.0083	-0.0034	0.0015	-0.0029	0.0036	0.0009	0.0036	0.0044	0.0172	0.0001	0.0004	0.0164	-0.0002	0.0188	30.163	-6.9925	62.9776
12	0.2852	0.2046	-0.3025	0.1471	-0.2177	0.3223	0.0177	-0.0119	0.013	0.0101	-0.0054	0.0094	-0.0128	0.0087	-0.0123	0.0242	-0.005	0.0006	0.0223	-0.0054	0.0118	24.7552	-9.5784	68.9773
13	0.3689	0.0004	-0.0488	0.1862	0.1028	0.5181	0.0197	-0.0088	-0.0253	-0.0568	-0.0055	-0.0743	-0.0208	-0.0249	-0.0143	0.0213	0.001	0.0202	0.0016	0.0013	0.0339	24.6432	-8.397	60.4992
14	0.0912	0.0761	0.0421	0.0889	0.0366	0.1011	0.0008	-0.0039	-0.0006	-0.0087	-0.0069	-0.0031	-0.0023	-0.0024	0.0061	0.0172	0.0002	0.0003	0.0148	0.0006	0.0158	33.2422	-2.5553	54.3762
15	0.8926	0.0185	0.3036	0.9241	0.1308	0.1208	0.0181	-0.0196	-0.0091	0.015	-0.0175	-0.0141	0.0068	-0.0065	-0.0006	0.0109	-0.001	-0.0037	0.0197	0.0086	0.0249	44.7312	-0.4661	64.1124
16	0.0821	0.1098	0.0233	3.48	1.1391	0.3749	0.006	0.0532	0.0125	-0.2781	-0.0026	-0.0085	-0.0933	-0.0093	-0.0034	0.025	0.0103	0.0045	0.0368	0.0129	0.0277	44.8452	4.0271	52.9961
17	0.3501	0.5036	0.1153	1.1278	0.4722	0.2706	0.0024	0.0099	0.0396	-0.0664	-0.012	0.0529	-0.051	-0.0179	0.0096	0.0248	-0.0003	-0.0012	0.0175	0.0019	0.0249	38.9688	4.0083	57.2471
18	7.9952	-0.1404	-2.1192	7.2795	6.8049	6.8558	-0.0006	0.5517	0.1357	-0.47	-0.2952	0.3537	-0.4379	-0.4111	0.2958	0.0365	0.0215	-0.0387	0.0535	-0.0146	0.0616	34.0167	22.0662	55.256

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 10
2	X-RAY DIFFRACTION	2	A	11 - 30
3	X-RAY DIFFRACTION	3	A	31 - 40
4	X-RAY DIFFRACTION	4	A	41 - 53
5	X-RAY DIFFRACTION	5	A	54 - 60
6	X-RAY DIFFRACTION	6	A	61 - 76
7	X-RAY DIFFRACTION	7	A	77 - 129
8	X-RAY DIFFRACTION	8	A	130 - 135
9	X-RAY DIFFRACTION	9	A	141 - 146
10	X-RAY DIFFRACTION	10	B	-2 - 5
11	X-RAY DIFFRACTION	11	B	6 - 29
12	X-RAY DIFFRACTION	12	B	30 - 44
13	X-RAY DIFFRACTION	13	B	45 - 61
14	X-RAY DIFFRACTION	14	B	62 - 88
15	X-RAY DIFFRACTION	15	B	89 - 98
16	X-RAY DIFFRACTION	16	B	99 - 109
17	X-RAY DIFFRACTION	17	B	110 - 132
18	X-RAY DIFFRACTION	18	B	133 - 142

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