PDB-5cj3: Crystal structure of the zorbamycin binding protein (ZbmA) from S...

ID or keywords:

Entry

Database: PDB / ID: 5cj3

Title

Crystal structure of the zorbamycin binding protein (ZbmA) from Streptomyces flavoviridis with zorbamycin

Components

Zbm binding protein

Keywords

Antibiotic binding protein/antibiotic / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / NatPro / zorbamycin binding protein / ENZYME DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS / ZORBAMYCIN / Antibiotic binding protein-antibiotic complex

Function / homology

Function and homology information

response to antibiotic
Similarity search - Function

Biological species

Streptomyces flavoviridis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6499 Å

Authors

Chang, C. / Bigelow, L. / Clancy, S. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Rudolf, J.D. / Ma, M. / Chang, C.-Y. / Lohman, J.R. ...

Citation

Journal: Biochemistry / Year: 2015
Title: Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892.
Authors: Rudolf, J.D. / Bigelow, L. / Chang, C. / Cuff, M.E. / Lohman, J.R. / Chang, C.Y. / Ma, M. / Yang, D. / Clancy, S. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.

History

Deposition	Jul 13, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2015	Group: Database references
Revision 1.2	Nov 25, 2015	Group: Database references
Revision 1.3	Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cj3.cif.gz	132.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5cj3.ent.gz	101.7 KB	Display	PDB format
PDBx/mmJSON format	5cj3.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/cj/5cj3 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/5cj3	HTTPS FTP

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Related structure data

Related structure data	4iagSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4mov-1 3e7b-2 1lmw-2 5ctn-1 6pqi-2 5e2f-1 5zqe-7 5zqe-8 6rr3-d 6obu-2 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-APC109219

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Zbm binding protein

B: Zbm binding protein

hetero molecules

32.8 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)	40.737, 78.989, 79.542
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Zbm binding protein Mass: 14880.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces flavoviridis (bacteria) / Gene: zbmA / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / References: UniProt: B9UIZ4
#2: Chemical	ChemComp-52G / Zorbamycin / (2R,3S,4S,5R,6R)-2-{[(2R,3S,4S,5S,6S)-2-{[(1R,2S)-2-[({6-amino-2-[(1S)-3-amino-1-{[(2S)-2,3-diamino-3-oxopropyl]amino}-3-oxopropyl]-5-methylpyrimidin-4-yl}carbonyl)amino]-3-{[(3R,4S,5S)-6-{[(2S)-1-({2-[(4'R)-4-{[(3E)-3-amino-3-iminopropyl]carbamoyl}-4',5'-dihydro-2,4'-bi-1,3-thiazol-2'-yl]ethyl}amino)-3-hydroxy-3-methyl-1-oxobutan-2-yl]amino}-1,4-dihydroxy-5-methyl-6-oxohexan-3-yl]amino}-1-(1H-imidazol-4-yl)-3-oxopropyl]oxy}-4,5-dihydroxy-6-methyltetrahydro-2H-pyran-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl carbamate (non-preferred name) Mass: 1412.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₅₅H₈₅N₁₉O₂₁S₂
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.15 Å³/Da / Density % sol: 42.79 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1M Sodium Phosphate-citrate pH 4.2, 40% Ethanol 5 % PEG1000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2014

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.6499→50 Å / Num. obs: 29473 / % possible obs: 93 % / Redundancy: 7.9 % / B_iso Wilson estimate: 12.66 Å² / R_merge(I) obs: 0.057 / R_pim(I) all: 0.021 / R_rim(I) all: 0.061 / Χ²: 0.896 / Net I/av σ(I): 34.653 / Net I/σ(I): 14.1 / Num. measured all: 234170

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.6499-1.66	5.6	0.374	603	0.931	0.17	0.413	0.603	79.8
1.66-1.68	5.9	0.346	652	0.954	0.15	0.379	0.616	82
1.68-1.69	6.1	0.35	676	0.939	0.15	0.383	0.6	85.2
1.69-1.71	6.2	0.314	686	0.95	0.134	0.343	0.626	90.1
1.71-1.73	6.5	0.336	719	0.95	0.138	0.365	0.741	94.4
1.73-1.74	6.9	0.288	766	0.964	0.114	0.31	0.667	98.6
1.74-1.76	7.3	0.246	790	0.985	0.094	0.264	0.676	100
1.76-1.78	7.6	0.242	799	0.979	0.091	0.259	0.655	100
1.78-1.8	8.1	0.217	765	0.985	0.079	0.231	0.692	100
1.8-1.82	8.6	0.193	761	0.992	0.068	0.205	0.679	100
1.82-1.84	8.8	0.177	813	0.994	0.062	0.188	0.688	100
1.84-1.86	8.8	0.153	769	0.993	0.054	0.163	0.665	100
1.86-1.88	8.8	0.201	758	0.992	0.07	0.213	1.017	100
1.88-1.9	7.8	0.219	664	0.993	0.078	0.233	1.299	83.5
1.9-1.93	3.8	0.115	329	0.902	0.064	0.133	3.764	41.4
1.93-1.96	8.2	0.211	760	0.989	0.076	0.225	1.725	97.4
1.96-1.98	8.9	0.105	761	0.997	0.037	0.111	0.726	100
1.98-2.01	8.8	0.089	797	0.996	0.031	0.094	0.684	100
2.01-2.05	8.8	0.081	793	0.997	0.028	0.086	0.676	100
2.05-2.08	6.7	0.109	779	0.99	0.042	0.117	1.773	99.7
2.08-2.11	8.3	0.074	778	0.997	0.026	0.079	0.777	99.7
2.11-2.15	8.8	0.062	792	0.996	0.022	0.066	0.638	100
2.15-2.19	8.9	0.058	780	0.997	0.021	0.062	0.646	100
2.19-2.24	7.8	0.059	555	0.996	0.022	0.063	0.707	69.6
2.24-2.29	5.3	0.062	437	0.984	0.03	0.069	1.027	55.8
2.29-2.34	8.8	0.05	787	0.998	0.018	0.053	0.664	100
2.34-2.4	8.8	0.047	805	0.998	0.017	0.05	0.654	100
2.4-2.46	8.9	0.044	768	0.998	0.016	0.047	0.633	100
2.46-2.54	8.8	0.044	813	0.998	0.016	0.047	0.704	100
2.54-2.62	8.8	0.041	775	0.998	0.014	0.043	0.642	100
2.62-2.71	8.7	0.051	820	0.998	0.018	0.055	1.165	100
2.71-2.82	8.8	0.041	776	0.997	0.015	0.044	0.812	100
2.82-2.95	8.7	0.041	813	0.997	0.014	0.043	0.85	100
2.95-3.11	8.7	0.043	793	0.997	0.016	0.046	1.039	100
3.11-3.3	8.6	0.046	818	0.997	0.016	0.049	1.283	100
3.3-3.55	8.1	0.05	800	0.995	0.018	0.053	1.656	99.5
3.55-3.91	5.8	0.044	436	0.997	0.018	0.048	1.505	53.8
3.91-4.48	7.7	0.037	787	0.997	0.014	0.04	1.121	94.5
4.48-5.64	8.1	0.037	830	0.996	0.013	0.039	1.083	99.2
5.64-50	7.4	0.044	870	0.997	0.016	0.047	1.311	95.7

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction
HKL-3000		phasing
SBC-Collect		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IAG

4iag

Resolution: 1.6499→35.522 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2127	3496	6.82 %
R_work	0.1759	47728	-
obs	0.1784	29164	85.85 %

Solvent computation

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

Displacement parameters

B_iso max: 70.29 Å² / B_iso mean: 17.1227 Å² / B_iso min: 4 Å²

Refinement step

Cycle: final / Resolution: 1.6499→35.522 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1958	0	392	165	2515
B_iso mean	-	-	21.68	26.08	-
Num. residues	-	-	-	-	252

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	2482
X-RAY DIFFRACTION	f_angle_d	1.788	3425
X-RAY DIFFRACTION	f_chiral_restr	0.083	402
X-RAY DIFFRACTION	f_plane_restr	0.008	423
X-RAY DIFFRACTION	f_dihedral_angle_d	18.685	1462

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6499-1.6725	0.2705	75	0.1947	1107	1182	50
1.6725-1.6964	0.2018	89	0.1891	1262	1351	56
1.6964-1.7217	0.2479	113	0.185	1402	1515	64
1.7217-1.7486	0.2073	124	0.1752	1630	1754	73
1.7486-1.7773	0.2587	139	0.1725	1823	1962	82
1.7773-1.808	0.2306	137	0.1794	1964	2101	89
1.808-1.8408	0.2307	157	0.1805	2063	2220	93
1.8408-1.8762	0.1988	164	0.1935	2093	2257	95
1.8762-1.9145	0.3116	103	0.2033	1462	1565	66
1.9145-1.9562	0.2654	116	0.2564	1601	1717	71
1.9562-2.0017	0.1976	163	0.1753	2180	2343	99
2.0017-2.0517	0.2076	161	0.1608	2217	2378	99
2.0517-2.1072	0.223	153	0.1862	2191	2344	98
2.1072-2.1692	0.2453	166	0.1671	2246	2412	100
2.1692-2.2392	0.2416	136	0.1731	1770	1906	80
2.2392-2.3192	0.2371	108	0.2107	1495	1603	68
2.3192-2.412	0.2253	173	0.1739	2239	2412	100
2.412-2.5218	0.2238	158	0.1712	2224	2382	100
2.5218-2.6547	0.2153	157	0.1825	2227	2384	100
2.6547-2.8209	0.2334	158	0.1809	2216	2374	100
2.8209-3.0386	0.2324	166	0.192	2238	2404	100
3.0386-3.3442	0.2202	159	0.1802	2222	2381	100
3.3442-3.8277	0.1954	110	0.1647	1582	1692	71
3.8277-4.8205	0.1373	155	0.1363	2088	2243	94
4.8205-35.5306	0.1794	156	0.1657	2186	2342	98

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	0.0771	-0.0045	-0.0375	0.0774	0.0051	0.0271	-0.0466	-0.0072	0.0262	0.1173	0.0281	-0.0078	-0.0084	0.0281	-0.0219	0.0698	0.0069	0.0466	0.0977	0.019	0.066	-3.403	-5.6638	27.3329
2	0.0087	-0.0068	0.0008	0.019	0.0067	0.0029	-0.0482	-0.0367	-0.0004	-0.0623	-0.0368	0.0021	-0.0932	-0.0337	-0.0169	0.0698	0.0185	-0.0106	0.0584	0.0079	0.0594	-2.3061	3.6613	10.078
3	0.0031	0.0026	-0.0028	0.0022	-0.0022	0.0028	-0.0051	0.0139	0.0217	0.0166	0.005	-0.0494	-0.0063	-0.0317	0.0004	0.0897	-0.0008	-0.0276	0.1013	-0.0145	0.1199	-0.5055	3.5382	15.717
4	0.0058	-0.0006	0.0001	0.0102	0.0041	0.0001	0.0175	-0.0156	-0.0123	0.0182	0.0477	0.0308	-0.0441	-0.0665	-0	0.0608	-0.0001	0.0009	0.0847	0.0089	0.0683	-2.4608	-0.7759	17.5714
5	0.0263	-0.0291	0.0614	0.033	-0.0698	0.1465	0.0284	0.0018	0.0195	-0.0148	0.0565	-0.022	-0.0153	0.0302	0.0162	0.0453	-0.0032	0.0265	0.0752	-0.0131	0.1137	13.0841	-6.2794	12.7203
6	0.0004	0.0032	-0.0016	0.0392	-0.0113	0.0033	0.0003	-0.0132	0.0031	-0.0321	0.0283	0.0351	0.0157	-0.0379	0.0266	0.0161	-0.0113	0	0.0871	0.0102	0.1017	-8.635	-12.0725	13.5462
7	0.0125	-0.0121	0.0129	0.0137	-0.0091	0.0131	0.0249	-0.0102	-0.0056	-0.1765	0.0093	0.0395	0.0523	0.0155	0.0001	0.1002	0.0167	0.0001	0.1141	-0.0049	0.0729	-5.3664	-9.2328	0.0524
8	0.0076	-0.0096	-0.0032	0.0092	0.003	0.0013	0.0193	0.0033	-0.0035	-0.0036	0.0346	-0.0152	0.0458	0.0259	0.0014	0.15	0.0168	-0.0019	0.0892	-0.0125	0.0736	-3.8422	-16.2272	4.562
9	0.0041	-0.0013	0.0095	0.003	-0.0006	0.0224	0.0528	0.0305	-0.004	0.0142	0.0407	0.0455	0.0799	-0.0372	0.0177	0.0489	-0.0153	-0.0028	0.0576	0.0058	0.0695	-4.8724	-13.4211	9.4114
10	0.0118	0.0053	-0.0083	0.0192	0.0153	0.0221	0.007	0.0209	-0.0161	0.0094	0.0079	0.0138	0.0698	-0.0437	-0.004	0.0273	0.007	-0.0204	0.0832	0.009	0.0953	-3.7271	-11.5876	18.2459
11	0.0066	0.0033	-0.0054	0.0103	0.0063	0.0115	0.0242	-0.0383	0.0055	0.0552	0.0503	-0.007	0.097	-0.077	0.0096	0.1254	-0.0023	0.0026	0.0618	0.0173	0.07	2.2756	-20.3979	30.1773
12	0.0065	0.0011	-0.0035	0.0052	0.0003	0.0041	0.0185	-0.0355	0.0014	-0.0269	0.0139	0.0055	0.0163	-0.0292	0.0035	0.1254	-0.0065	0.034	0.0903	0.0116	0.0821	0.8298	-20.1046	24.198
13	0.0102	0.0066	-0.0097	0.0111	0	0.013	0.0392	-0.0015	-0.0067	0.0238	0.0438	0.0559	0.0239	-0.0277	0.0034	0.0755	0.013	0.0176	0.0756	0.0206	0.0883	-1.4279	-15.5229	23.7661
14	0.0058	-0.0015	0.0037	0.0148	0.0017	0.003	0.0045	0.0262	0.0106	-0.0021	0.0052	-0.0186	0.0093	0.0156	0.0049	0.0135	0.0137	-0.0082	0.1061	-0.0311	0.1388	14.7542	-11.6217	19.7665
15	0.0507	0.1027	-0.0693	0.1918	-0.1229	0.1181	-0.0217	-0.071	0.0489	0.2183	0.0973	-0.025	-0.0452	-0.0419	0.0976	0.1457	0.0434	-0.0062	0.1103	-0.0151	0.0647	1.9913	-6.2654	36.4433
16	0.0659	0.0163	-0.0304	0.1088	0.0576	0.057	-0.0083	0.0086	-0.0297	0.0792	0.0494	-0.0506	-0.1071	-0.045	0.0616	0.0824	0.0945	0.01	-0.0259	-0.0811	0.0315	1.8621	-1.3075	32.4943

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 15 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 35 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 43 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 44 through 52 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 53 through 61 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 62 through 70 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 71 through 90 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 91 through 102 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 103 through 123 )	A
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 15 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 16 through 35 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 36 through 43 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 44 through 52 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 53 through 61 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 62 through 89 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 90 through 126 )	B

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About Yorodumi

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Yorodumi