PDB-9g9q: Crystal structure of PbdA bound to p-methoxybenzoate.

ID or keywords:

Entry

Database: PDB / ID: 9g9q

Title

Crystal structure of PbdA bound to p-methoxybenzoate.

Components

Cytochrome P450 CYP199

Keywords

OXIDOREDUCTASE / Cytochrome P450

Function / homology

Function and homology information

Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / 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

Rhodococcus jostii RHA1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 Å

Authors

Hinchen, D.J. / Wolf, M.E. / Eltis, L.D. / McGeehan, J.E.

Funding support

United States,

United Kingdom, 2items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Characterization of a cytochrome P450 that catalyzes the O-demethylation of lignin-derived benzoates.
Authors: Wolf, M.E. / Hinchen, D.J. / McGeehan, J.E. / Eltis, L.D.

History

Deposition	Jul 25, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 2, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Database references / Structure summary / Category: citation / pdbx_entry_details Item: _citation.journal_volume / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9g9q.cif.gz	725 KB	Display	PDBx/mmCIF format
PDB format	pdb9g9q.ent.gz	490.7 KB	Display	PDB format
PDBx/mmJSON format	9g9q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g9/9g9q ftp://data.pdbj.org/pub/pdb/validation_reports/g9/9g9q	HTTPS FTP

-
Related structure data

Related structure data	9g9rC 9g9sC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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 CYP199

B: Cytochrome P450 CYP199

hetero molecules

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

1

A: Cytochrome P450 CYP199

hetero molecules

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

2

B: Cytochrome P450 CYP199

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.17, 55.11, 64.26
Angle α, β, γ (deg.)	99.87, 94.9, 103.24
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 8 - 399 / Label seq-ID: 28 - 419

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Cytochrome P450 CYP199 Mass: 45972.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: RHA1_ro02948 / Production host: Escherichia coli (E. coli) References: UniProt: Q0SCI3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M HEPES pH 7.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 7, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.03→52.595 Å / Num. obs: 43063 / % possible obs: 97.92 % / Redundancy: 3.57 % / CC_1/2: 0.99 / R_merge(I) obs: 0.1713 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.03→2.07 Å / Redundancy: 3.6 % / R_merge(I) obs: 1.553 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 2096 / CC_1/2: 0.304 / R_pim(I) all: 0.95 / % possible all: 96.46

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.77)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.03→52.595 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.926 / SU B: 21.552 / SU ML: 0.234 / Cross valid method: FREE R-VALUE / ESU R Free: 0.214
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2575	2174	5.049 %
R_work	0.1641	40887	-
all	0.169	-	-
obs	-	43061	97.915 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.606 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.466 Å²	-1.038 Å²	-0.113 Å²
2-	-	-0.509 Å²	-0.878 Å²
3-	-	-	0.944 Å²

Refinement step

Cycle: LAST / Resolution: 2.03→52.595 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6014	0	150	360	6524

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	6335
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	5812
X-RAY DIFFRACTION	r_angle_refined_deg	2.202	1.82	8687
X-RAY DIFFRACTION	r_angle_other_deg	0.901	1.749	13300
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.09	5	785
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.652	5	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.933	10	864
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.31	10	289
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	946
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	7779
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	1545
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1390
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.164	0.2	5712
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	3095
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	3411
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	312
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.188	0.2	34
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	124
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.221	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	6.979	2.262	3146
X-RAY DIFFRACTION	r_mcbond_other	6.979	2.262	3146
X-RAY DIFFRACTION	r_mcangle_it	10.27	4.072	3929
X-RAY DIFFRACTION	r_mcangle_other	10.269	4.072	3930
X-RAY DIFFRACTION	r_scbond_it	7.196	2.425	3189
X-RAY DIFFRACTION	r_scbond_other	7.195	2.425	3190
X-RAY DIFFRACTION	r_scangle_it	10.458	4.382	4758
X-RAY DIFFRACTION	r_scangle_other	10.456	4.382	4759
X-RAY DIFFRACTION	r_lrange_it	14.786	25.509	7197
X-RAY DIFFRACTION	r_lrange_other	14.482	25.001	7142
X-RAY DIFFRACTION	r_rigid_bond_restr	4.986	3	12147
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	12389

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0977	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.0977	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.03-2.083	0.395	168	0.328	2976	0.332	3275	0.897	0.923	96	0.329
2.083-2.14	0.342	155	0.288	2909	0.291	3152	0.915	0.942	97.2081	0.285
2.14-2.202	0.337	154	0.265	2839	0.269	3073	0.929	0.955	97.3967	0.258
2.202-2.269	0.332	151	0.257	2765	0.261	3004	0.906	0.956	97.0706	0.247
2.269-2.344	0.292	164	0.216	2638	0.221	2872	0.943	0.971	97.5627	0.2
2.344-2.426	0.286	157	0.199	2586	0.204	2804	0.945	0.975	97.8245	0.183
2.426-2.517	0.302	140	0.181	2514	0.187	2715	0.943	0.981	97.7532	0.162
2.517-2.619	0.272	103	0.169	2458	0.173	2614	0.958	0.984	97.9725	0.149
2.619-2.736	0.302	117	0.162	2341	0.168	2506	0.943	0.985	98.0846	0.139
2.736-2.869	0.271	114	0.149	2237	0.156	2389	0.958	0.987	98.4094	0.128
2.869-3.023	0.236	113	0.145	2114	0.15	2270	0.959	0.987	98.1057	0.124
3.023-3.206	0.293	90	0.141	2030	0.148	2152	0.948	0.988	98.513	0.12
3.206-3.427	0.26	112	0.135	1871	0.142	2012	0.958	0.989	98.5586	0.118
3.427-3.7	0.193	80	0.116	1771	0.12	1880	0.979	0.992	98.4575	0.104
3.7-4.051	0.219	79	0.122	1625	0.126	1727	0.972	0.991	98.6682	0.113
4.051-4.526	0.208	77	0.117	1479	0.122	1569	0.978	0.992	99.1714	0.111
4.526-5.22	0.18	77	0.116	1289	0.12	1376	0.985	0.993	99.2733	0.114
5.22-6.377	0.256	60	0.151	1099	0.157	1170	0.968	0.989	99.0598	0.143
6.377-8.953	0.223	40	0.146	860	0.149	905	0.976	0.988	99.4475	0.144
8.953-52.595	0.158	23	0.167	486	0.166	512	0.987	0.983	99.4141	0.179

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	1.0234	-0.2077	-0.2831	0.6973	0.1845	0.7028	0.0117	0.0768	0.0576	-0.0208	-0.0209	0.0163	-0.0061	-0.0837	0.0092	0.004	-0.0067	-0.0032	0.0298	0.0092	0.008	-5.6168	16.404	11.2559
2	0.2264	0.0974	-0.1702	0.9089	0.3995	0.8897	0.0089	0.0511	-0.0089	-0.0863	-0.0107	0.0462	0.0114	-0.0458	0.0018	0.0274	0.0129	-0.0035	0.0509	0.0164	0.018	-24.9094	3.3822	-19.9585

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	8 - 400	28 - 420
2	2	B	B	7 - 400	27 - 420

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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