PDB-6hnn: Crystal structure of wild-type IdmH, a putative polyketide cyclas...

ID or keywords:

Entry

Database: PDB / ID: 6hnn

Title

Crystal structure of wild-type IdmH, a putative polyketide cyclase from Streptomyces antibioticus

Components

Putative polyketide cyclase IdmH

Keywords

BIOSYNTHETIC PROTEIN / Polyketide synthesis / putative cyclase

Function / homology

polyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / NTF2-like domain superfamily / Uncharacterized protein idmH

Function and homology information

Biological species

Streptomyces antibioticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Drulyte, I. / Obajdin, J. / Trinh, C. / Hemsworth, G.R. / Berry, A.

Funding support

United Kingdom, 1items

Citation

Journal: Iucrj / Year: 2019
Title: Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase.
Authors: Drulyte, I. / Obajdin, J. / Trinh, C.H. / Kalverda, A.P. / van der Kamp, M.W. / Hemsworth, G.R. / Berry, A.

History

Deposition	Sep 16, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2019	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6hnn.cif.gz	263.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6hnn.ent.gz	211.5 KB	Display	PDB format
PDBx/mmJSON format	6hnn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6hnn_validation.pdf.gz	488.8 KB	Display	wwPDB validaton report
Full document	6hnn_full_validation.pdf.gz	496.5 KB	Display
Data in XML	6hnn_validation.xml.gz	45.3 KB	Display
Data in CIF	6hnn_validation.cif.gz	61.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hn/6hnn ftp://data.pdbj.org/pub/pdb/validation_reports/hn/6hnn	HTTPS FTP

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Related structure data

Related structure data	6hnlC 6hnmSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5nnu-3 4qbx-d 6syw-d 6f81-d 3onc-d 2dv0-d 5yi6-4 5yi6-2 3q67-2 7e2m-2 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) 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

6hnlC

6hnmSC

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Putative polyketide cyclase IdmH

B: Putative polyketide cyclase IdmH

C: Putative polyketide cyclase IdmH

D: Putative polyketide cyclase IdmH

E: Putative polyketide cyclase IdmH

F: Putative polyketide cyclase IdmH

G: Putative polyketide cyclase IdmH

H: Putative polyketide cyclase IdmH

I: Putative polyketide cyclase IdmH

J: Putative polyketide cyclase IdmH

162 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative polyketide cyclase IdmH

B: Putative polyketide cyclase IdmH

defined by author&software
Evidence: gel filtration, Confirmed by PISA analysis
32.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Putative polyketide cyclase IdmH

D: Putative polyketide cyclase IdmH

defined by author&software
Evidence: gel filtration, Confirmed by PISA analysis
32.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Putative polyketide cyclase IdmH

F: Putative polyketide cyclase IdmH

defined by author&software
Evidence: gel filtration, Confirmed by PISA analysis
32.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Putative polyketide cyclase IdmH

H: Putative polyketide cyclase IdmH

defined by author&software
Evidence: gel filtration, Confirmed by PISA analysis
32.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Putative polyketide cyclase IdmH

J: Putative polyketide cyclase IdmH

defined by author&software
Evidence: gel filtration, Confirmed by PISA analysis
32.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.684, 103.519, 99.584
Angle α, β, γ (deg.)	90.00, 91.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	LEU	LEU	A	A	6 - 142	6 - 142
2	1	HIS	HIS	LEU	LEU	C	C	6 - 142	6 - 142
1	2	HIS	HIS	LEU	LEU	A	A	6 - 142	6 - 142
2	2	HIS	HIS	LEU	LEU	B	B	6 - 142	6 - 142
1	3	HIS	HIS	GLY	GLY	A	A	6 - 143	6 - 143
2	3	HIS	HIS	GLY	GLY	D	D	6 - 143	6 - 143
1	4	GLN	GLN	GLY	GLY	A	A	7 - 143	7 - 143
2	4	GLN	GLN	GLY	GLY	G	G	7 - 143	7 - 143
1	5	GLN	GLN	GLY	GLY	A	A	7 - 143	7 - 143
2	5	GLN	GLN	GLY	GLY	E	E	7 - 143	7 - 143
1	6	GLN	GLN	GLN	GLN	A	A	7 - 141	7 - 141
2	6	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
1	7	HIS	HIS	GLY	GLY	A	A	6 - 143	6 - 143
2	7	HIS	HIS	GLY	GLY	H	H	6 - 143	6 - 143
1	8	HIS	HIS	GLY	GLY	A	A	6 - 143	6 - 143
2	8	HIS	HIS	GLY	GLY	I	I	6 - 143	6 - 143
1	9	GLN	GLN	GLY	GLY	A	A	7 - 143	7 - 143
2	9	GLN	GLN	GLY	GLY	J	J	7 - 143	7 - 143
1	10	HIS	HIS	GLY	GLY	C	C	6 - 143	6 - 143
2	10	HIS	HIS	GLY	GLY	B	B	6 - 143	6 - 143
1	11	HIS	HIS	LEU	LEU	C	C	6 - 142	6 - 142
2	11	HIS	HIS	LEU	LEU	D	D	6 - 142	6 - 142
1	12	GLN	GLN	LEU	LEU	C	C	7 - 142	7 - 142
2	12	GLN	GLN	LEU	LEU	G	G	7 - 142	7 - 142
1	13	GLN	GLN	LEU	LEU	C	C	7 - 142	7 - 142
2	13	GLN	GLN	LEU	LEU	E	E	7 - 142	7 - 142
1	14	GLN	GLN	GLN	GLN	C	C	7 - 141	7 - 141
2	14	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
1	15	HIS	HIS	LEU	LEU	C	C	6 - 142	6 - 142
2	15	HIS	HIS	LEU	LEU	H	H	6 - 142	6 - 142
1	16	HIS	HIS	LEU	LEU	C	C	6 - 142	6 - 142
2	16	HIS	HIS	LEU	LEU	I	I	6 - 142	6 - 142
1	17	GLN	GLN	LEU	LEU	C	C	7 - 142	7 - 142
2	17	GLN	GLN	LEU	LEU	J	J	7 - 142	7 - 142
1	18	HIS	HIS	LEU	LEU	B	B	6 - 142	6 - 142
2	18	HIS	HIS	LEU	LEU	D	D	6 - 142	6 - 142
1	19	GLN	GLN	LEU	LEU	B	B	7 - 142	7 - 142
2	19	GLN	GLN	LEU	LEU	G	G	7 - 142	7 - 142
1	20	GLN	GLN	LEU	LEU	B	B	7 - 142	7 - 142
2	20	GLN	GLN	LEU	LEU	E	E	7 - 142	7 - 142
1	21	GLN	GLN	GLN	GLN	B	B	7 - 141	7 - 141
2	21	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
1	22	HIS	HIS	LEU	LEU	B	B	6 - 142	6 - 142
2	22	HIS	HIS	LEU	LEU	H	H	6 - 142	6 - 142
1	23	HIS	HIS	LEU	LEU	B	B	6 - 142	6 - 142
2	23	HIS	HIS	LEU	LEU	I	I	6 - 142	6 - 142
1	24	GLN	GLN	LEU	LEU	B	B	7 - 142	7 - 142
2	24	GLN	GLN	LEU	LEU	J	J	7 - 142	7 - 142
1	25	GLN	GLN	GLY	GLY	D	D	7 - 143	7 - 143
2	25	GLN	GLN	GLY	GLY	G	G	7 - 143	7 - 143
1	26	GLN	GLN	GLY	GLY	D	D	7 - 143	7 - 143
2	26	GLN	GLN	GLY	GLY	E	E	7 - 143	7 - 143
1	27	GLN	GLN	GLN	GLN	D	D	7 - 141	7 - 141
2	27	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
1	28	HIS	HIS	VAL	VAL	D	D	6 - 144	6 - 144
2	28	HIS	HIS	VAL	VAL	H	H	6 - 144	6 - 144
1	29	HIS	HIS	VAL	VAL	D	D	6 - 144	6 - 144
2	29	HIS	HIS	VAL	VAL	I	I	6 - 144	6 - 144
1	30	GLN	GLN	GLY	GLY	D	D	7 - 143	7 - 143
2	30	GLN	GLN	GLY	GLY	J	J	7 - 143	7 - 143
1	31	GLN	GLN	VAL	VAL	G	G	7 - 144	7 - 144
2	31	GLN	GLN	VAL	VAL	E	E	7 - 144	7 - 144
1	32	GLN	GLN	GLN	GLN	G	G	7 - 141	7 - 141
2	32	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
1	33	GLN	GLN	GLY	GLY	G	G	7 - 143	7 - 143
2	33	GLN	GLN	GLY	GLY	H	H	7 - 143	7 - 143
1	34	GLN	GLN	GLY	GLY	G	G	7 - 143	7 - 143
2	34	GLN	GLN	GLY	GLY	I	I	7 - 143	7 - 143
1	35	GLN	GLN	VAL	VAL	G	G	7 - 144	7 - 144
2	35	GLN	GLN	VAL	VAL	J	J	7 - 144	7 - 144
1	36	GLN	GLN	GLN	GLN	E	E	7 - 141	7 - 141
2	36	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
1	37	GLN	GLN	GLY	GLY	E	E	7 - 143	7 - 143
2	37	GLN	GLN	GLY	GLY	H	H	7 - 143	7 - 143
1	38	GLN	GLN	GLY	GLY	E	E	7 - 143	7 - 143
2	38	GLN	GLN	GLY	GLY	I	I	7 - 143	7 - 143
1	39	GLN	GLN	VAL	VAL	E	E	7 - 144	7 - 144
2	39	GLN	GLN	VAL	VAL	J	J	7 - 144	7 - 144
1	40	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
2	40	GLN	GLN	GLN	GLN	H	H	7 - 141	7 - 141
1	41	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
2	41	GLN	GLN	GLN	GLN	I	I	7 - 141	7 - 141
1	42	GLN	GLN	GLN	GLN	F	F	7 - 141	7 - 141
2	42	GLN	GLN	GLN	GLN	J	J	7 - 141	7 - 141
1	43	HIS	HIS	VAL	VAL	H	H	6 - 144	6 - 144
2	43	HIS	HIS	VAL	VAL	I	I	6 - 144	6 - 144
1	44	GLN	GLN	GLY	GLY	H	H	7 - 143	7 - 143
2	44	GLN	GLN	GLY	GLY	J	J	7 - 143	7 - 143
1	45	GLN	GLN	GLY	GLY	I	I	7 - 143	7 - 143
2	45	GLN	GLN	GLY	GLY	J	J	7 - 143	7 - 143

NCS ensembles :

#1: Protein	Putative polyketide cyclase IdmH Mass: 16158.217 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: idmH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5HV10
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.13 Å³/Da / Density % sol: 42.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M calcium acetate, 0.1 MES, 18.6% (w/v) polyethylene glycol 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.7→51.76 Å / Num. obs: 37144 / % possible obs: 99.6 % / Redundancy: 4.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.086 / R_pim(I) all: 0.046 / R_rim(I) all: 0.097 / Net I/σ(I): 11.4
Reflection shell	Resolution: 2.7→2.82 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4498 / CC_1/2: 0.655 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
TRUNCATE		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6HNM

6hnm

Resolution: 2.7→51.76 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.93 / SU B: 15.375 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24421	1832	4.9 %	RANDOM
R_work	0.2107	-	-	-
obs	0.21232	35294	99.54 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 69.399 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.69 Å²	0 Å²	-2.64 Å²
2-	-	2.23 Å²	0 Å²
3-	-	-	-2.76 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→51.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10265	0	0	9	10274

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	10526
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9410
X-RAY DIFFRACTION	r_angle_refined_deg	1.472	1.943	14415
X-RAY DIFFRACTION	r_angle_other_deg	0.961	3	21676
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.971	5	1374
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.58	23.168	423
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.688	15	1466
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.378	15	74
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	1661
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	11966
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2172
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	5.598	7.094	5526
X-RAY DIFFRACTION	r_mcbond_other	5.596	7.094	5525
X-RAY DIFFRACTION	r_mcangle_it	8.398	10.644	6890
X-RAY DIFFRACTION	r_mcangle_other	8.398	10.644	6891
X-RAY DIFFRACTION	r_scbond_it	5.828	7.38	5000
X-RAY DIFFRACTION	r_scbond_other	5.828	7.38	5000
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	8.787	10.914	7525
X-RAY DIFFRACTION	r_long_range_B_refined	11.771	83.808	10936
X-RAY DIFFRACTION	r_long_range_B_other	11.771	83.811	10936
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	7906	0.06
1	2	C	7906	0.06
2	1	A	7984	0.06
2	2	B	7984	0.06
3	1	A	8174	0.04
3	2	D	8174	0.04
4	1	A	8064	0.06
4	2	G	8064	0.06
5	1	A	8094	0.04
5	2	E	8094	0.04
6	1	A	7870	0.06
6	2	F	7870	0.06
7	1	A	8026	0.07
7	2	H	8026	0.07
8	1	A	7782	0.06
8	2	I	7782	0.06
9	1	A	7758	0.05
9	2	J	7758	0.05
10	1	C	8090	0.05
10	2	B	8090	0.05
11	1	C	7978	0.04
11	2	D	7978	0.04
12	1	C	7840	0.06
12	2	G	7840	0.06
13	1	C	7836	0.05
13	2	E	7836	0.05
14	1	C	7936	0.04
14	2	F	7936	0.04
15	1	C	8096	0.05
15	2	H	8096	0.05
16	1	C	7898	0.04
16	2	I	7898	0.04
17	1	C	7548	0.05
17	2	J	7548	0.05
18	1	B	8012	0.05
18	2	D	8012	0.05
19	1	B	7896	0.06
19	2	G	7896	0.06
20	1	B	7916	0.05
20	2	E	7916	0.05
21	1	B	8024	0.02
21	2	F	8024	0.02
22	1	B	8188	0.04
22	2	H	8188	0.04
23	1	B	7900	0.04
23	2	I	7900	0.04
24	1	B	7572	0.06
24	2	J	7572	0.06
25	1	D	8158	0.04
25	2	G	8158	0.04
26	1	D	8096	0.03
26	2	E	8096	0.03
27	1	D	7874	0.05
27	2	F	7874	0.05
28	1	D	8082	0.06
28	2	H	8082	0.06
29	1	D	7882	0.05
29	2	I	7882	0.05
30	1	D	7798	0.04
30	2	J	7798	0.04
31	1	G	8070	0.04
31	2	E	8070	0.04
32	1	G	7806	0.06
32	2	F	7806	0.06
33	1	G	7926	0.06
33	2	H	7926	0.06
34	1	G	7696	0.06
34	2	I	7696	0.06
35	1	G	7780	0.04
35	2	J	7780	0.04
36	1	E	7826	0.05
36	2	F	7826	0.05
37	1	E	7920	0.06
37	2	H	7920	0.06
38	1	E	7682	0.06
38	2	I	7682	0.06
39	1	E	7766	0.04
39	2	J	7766	0.04
40	1	F	8026	0.03
40	2	H	8026	0.03
41	1	F	7862	0.02
41	2	I	7862	0.02
42	1	F	7502	0.05
42	2	J	7502	0.05
43	1	H	8006	0.04
43	2	I	8006	0.04
44	1	H	7642	0.06
44	2	J	7642	0.06
45	1	I	7484	0.06
45	2	J	7484	0.06

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.345	140	-
R_work	0.357	2587	-
obs	-	-	99.02 %

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