PDB-4bf4: PikC D50N mutant in complex with the engineered cycloalkane subst...

ID or keywords:

Entry

Database: PDB / ID: 4bf4

Title

PikC D50N mutant in complex with the engineered cycloalkane substrate mimic bearing a termianl N,N-dimethylamino group

Components

CYTOCHROME P450 HYDROXYLASE PIKC

Keywords

OXIDOREDUCTASE / MONOOXYGENASE / PIKROMYCIN BIOSYNTHESIS

Function / homology

Function and homology information

pikromycin synthase / macrolide biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function

Biological species

STREPTOMYCES VENEZUELAE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Podust, L.M.

Citation

Journal: To be Published
Title: Recognition of Synthetic Substrates by P450 Pikc
Authors: Podust, L.M.

History

Deposition	Mar 14, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	4bf4.cif.gz	2.4 MB	Display	PDBx/mmCIF format
PDB format	pdb4bf4.ent.gz	2 MB	Display	PDB format
PDBx/mmJSON format	4bf4.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4bf4_validation.pdf.gz	5.9 MB	Display	wwPDB validaton report
Full document	4bf4_full_validation.pdf.gz	6 MB	Display
Data in XML	4bf4_validation.xml.gz	228.3 KB	Display
Data in CIF	4bf4_validation.cif.gz	303.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bf/4bf4 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bf4	HTTPS FTP

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Related structure data

Related structure data	3zpiC 4b7dC 4umzC 2bvjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3zk5-1 2xc3-d 6f0c-d 4b7d-2 3zpi-1 2whw-2 4b7s-2 4ego-4 2xn8-d 2bvj-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) 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) 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) 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#82 - Oct 2006 Cytochrome p450 similarity (1)

Deposited unit

A: CYTOCHROME P450 HYDROXYLASE PIKC

B: CYTOCHROME P450 HYDROXYLASE PIKC

C: CYTOCHROME P450 HYDROXYLASE PIKC

D: CYTOCHROME P450 HYDROXYLASE PIKC

E: CYTOCHROME P450 HYDROXYLASE PIKC

F: CYTOCHROME P450 HYDROXYLASE PIKC

G: CYTOCHROME P450 HYDROXYLASE PIKC

H: CYTOCHROME P450 HYDROXYLASE PIKC

I: CYTOCHROME P450 HYDROXYLASE PIKC

J: CYTOCHROME P450 HYDROXYLASE PIKC

K: CYTOCHROME P450 HYDROXYLASE PIKC

L: CYTOCHROME P450 HYDROXYLASE PIKC

M: CYTOCHROME P450 HYDROXYLASE PIKC

N: CYTOCHROME P450 HYDROXYLASE PIKC

O: CYTOCHROME P450 HYDROXYLASE PIKC

P: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

784 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

2

B: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

3

C: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

4

D: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

5

E: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

6

F: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

7

G: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

8

H: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

9

I: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

10

J: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

11

K: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

12

L: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

13

M: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

14

N: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

15

O: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

16

P: CYTOCHROME P450 HYDROXYLASE PIKC

hetero molecules

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

Unit cell

Length a, b, c (Å)	110.273, 130.113, 134.898
Angle α, β, γ (deg.)	66.48, 70.25, 72.23
Int Tables number	1
Space group name H-M	P1

#1: Protein	CYTOCHROME P450 HYDROXYLASE PIKC / CYTOCHROME P450 MONOOXYGENASE Mass: 48267.758 Da / Num. of mol.: 16 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: O87605
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-17Q / 1.7.6 5-cyclododecyloxy-N,N-dimethyl-pentan-1-amine Mass: 297.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₃₉NO
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	1.7.6 5-CYCLODODECYLOXY-N,N-DIMETHYL-PENTAN-1-AMINE (17Q): ENGINEERED SUBSTRATRATE MIMIC

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.6 % / Description: NONE
Crystal grow	pH: 6.5 Details: 27% PEG3350, 0.2 M LI SULFATE, 0.1 M NA CACODILATE, PH 6.5

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
Detector	Type: MARRESEARCH / Detector: CCD / Date: Sep 29, 2012 / Details: MIRRORS
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11587 Å / Relative weight: 1
Reflection	Resolution: 2.7→119.84 Å / Num. obs: 169609 / % possible obs: 97.4 % / Observed criterion σ(I): 1.5 / Redundancy: 2.1 % / B_iso Wilson estimate: 63.2 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 5.9
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVJ

2bvj

Resolution: 2.7→119.84 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.874 / SU B: 37.957 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27903	8479	5 %	RANDOM
R_work	0.1959	-	-	-
obs	0.20009	161093	97.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 45.865 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.39 Å²	0.71 Å²	-0.68 Å²
2-	-	0.01 Å²	-0.53 Å²
3-	-	-	0.83 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→119.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	48831	0	790	514	50135

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	51118
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.464	2.023	70079
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.171	5	6379
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.744	22.284	2237
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.829	15	7742
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.318	15	576
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	7786
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.022	39754
X-RAY DIFFRACTION	r_gen_planes_other
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	0.96	1.5	31981
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.771	2	51472
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.025	3	19137
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.344	4.5	18607
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	1.069		51118
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.423	607	-
R_work	0.303	11790	-
obs	-	-	96.65 %

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	0.2603	0.0785	0.0333	0.367	-0.0682	0.2635	0.0142	-0.0075	-0.024	-0.0031	-0.0006	0.0423	0.0241	-0.0045	-0.0136	0.0937	0.0099	0.0122	0.0886	0.0161	0.1083	13.996	-17.443	-14.612
2	0.1348	-0.0157	0.0453	0.5702	-0.0276	0.3002	0.035	0.0084	-0.034	-0.0311	-0.0165	0.0588	0.0167	-0.0175	-0.0186	0.1101	0.0037	0.0158	0.0908	0.0171	0.1089	48.729	-60.598	-43.166
3	0.3888	0.0271	-0.008	0.2598	-0.166	0.2114	0.0078	0.0197	0.0069	-0.0012	-0.0032	-0.0328	0.0046	0.0405	-0.0047	0.1065	0.0106	0.0215	0.0834	-0.0004	0.1052	16.151	30.775	-18.181
4	0.2741	0.0689	0.0274	0.2242	-0.1049	0.2829	-0.0122	-0.0023	0.027	-0.0043	0.0051	-0.0066	0.0017	0.0412	0.0071	0.105	0.0154	0.0078	0.0858	0.0117	0.1003	51.877	-50.326	11.489
5	0.4688	-0.0831	-0.1038	0.3167	0.0125	0.3008	-0.0223	-0.0023	0.0534	0.0029	0.0099	-0.0319	0.0214	0.0376	0.0124	0.097	0.0154	0.0205	0.1051	0.0125	0.0825	50.426	-12.774	-46.341
6	0.2832	0.1156	0.3487	0.5579	0.3299	0.6889	0.0207	-0.0021	0.0187	0.0498	-0.0161	-0.0228	-0.0025	0.0391	-0.0046	0.1097	0.0088	0.0171	0.0715	0.0009	0.1111	18.702	-74.765	-10.331
7	0.456	-0.0314	0.0817	0.1383	0.0404	0.2811	-0.0458	0.0082	0.003	0.0152	0.0212	0.0156	-0.0097	0.0004	0.0246	0.1098	-0.0004	0.0149	0.0817	0.0197	0.105	56.63	-5.625	-0.96
8	0.2379	-0.0266	-0.0717	0.5513	0.0122	0.3	-0.0172	-0.0039	-0.0171	-0.0008	0.0174	0.0726	0.033	0.0168	-0.0002	0.1046	0.0138	0.0229	0.0908	0.0188	0.0988	50.766	-98.921	12.789
9	0.5572	0.1726	0.1887	0.1726	0.0383	0.2418	0.0554	-0.0043	-0.1308	0.0059	-0.0205	-0.0619	-0.0593	-0.005	-0.035	0.0963	0.0016	0.0149	0.0857	0.0198	0.1427	93.44	6.532	-42.022
10	0.449	-0.2593	0.0917	1.0059	-0.0098	0.347	-0.0225	0.0031	-0.0355	0.0324	0.0299	0.1122	0.0132	0.0248	-0.0074	0.0968	0.0315	0.0207	0.0919	0.0069	0.1081	18.108	-58.716	44.068
11	0.6893	-0.1435	0.0131	0.2302	-0.1763	0.3341	0.0429	0.0143	0.0093	-0.0232	0.0265	0.0719	-0.0089	-0.013	-0.0694	0.1059	-0.005	0.0019	0.0792	0.009	0.1717	92.404	-48.82	-28.906
12	0.854	-0.2812	0.154	0.2145	-0.2884	0.7386	-0.0482	0.0649	0.0052	0.0727	0.0387	-0.054	-0.122	-0.1596	0.0096	0.1159	0.0406	0.0053	0.1416	0.0002	0.0819	15.727	-90.408	-55.711
13	0.6599	-0.442	-0.1719	0.9012	-0.2258	0.7076	0.1503	0.0281	0.0618	-0.1065	-0.1238	-0.0035	0.0698	0.1061	-0.0265	0.1374	0.0537	0.0142	0.1068	0.0084	0.0854	18.464	-10.875	43.456
14	0.2885	-0.0133	0.6098	-0.0694	0.0299	1.5732	-0.1083	-0.0535	-0.0407	0.0192	-0.0507	-0.0396	-0.1408	-0.3695	0.159	0.0825	0.0688	-0.0297	0.2455	-0.1269	0.2211	93.56	-88.782	32.189
15	0.0976	-0.0589	-0.0213	0.8718	0.0311	0.558	-0.004	-0.006	0.0112	0.0994	0.0998	-0.2325	-0.0399	-0.0417	-0.0958	0.0894	0.0111	-0.0248	0.1108	-0.0424	0.2067	92.891	-31.429	16.451
16	1.2956	-0.1752	-0.0619	0.189	-0.0986	0.1483	-0.1817	-0.556	0.1198	-0.0547	0.0739	-0.0035	-0.0149	-0.0094	0.1079	0.1094	0.1226	-0.0314	0.3966	-0.0932	0.0921	61.955	9.939	44.542

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	11 - 406
2	X-RAY DIFFRACTION	2	B	11 - 406
3	X-RAY DIFFRACTION	3	C	11 - 406
4	X-RAY DIFFRACTION	4	D	11 - 406
5	X-RAY DIFFRACTION	5	E	11 - 406
6	X-RAY DIFFRACTION	6	F	11 - 406
7	X-RAY DIFFRACTION	7	G	11 - 406
8	X-RAY DIFFRACTION	8	H	11 - 406
9	X-RAY DIFFRACTION	9	I	11 - 406
10	X-RAY DIFFRACTION	10	J	11 - 406
11	X-RAY DIFFRACTION	11	K	11 - 406
12	X-RAY DIFFRACTION	12	L	11 - 406
13	X-RAY DIFFRACTION	13	M	11 - 406
14	X-RAY DIFFRACTION	14	N	11 - 406
15	X-RAY DIFFRACTION	15	O	11 - 406
16	X-RAY DIFFRACTION	16	P	11 - 406

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi