PDB-8xhp: The apo structure of SsBcmC

ID or keywords:

Entry

Database: PDB / ID: 8xhp

Title

The apo structure of SsBcmC

Components

Fe/2OG dependent dioxygenase

Keywords

OXIDOREDUCTASE / Fe/2OG dependent dioxygenase / bicyclomycin / hydroxylation

Function / homology

2-OXOGLUTARIC ACID / :

Function and homology information

Biological species

Streptomyces cinnamoneus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.86000825296 Å

Authors

Wu, L. / Tang, G.L. / Zhou, J.H.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2025
Title: Three distinct strategies lead to programmable aliphatic C-H oxidation in bicyclomycin biosynthesis.
Authors: Wu, L. / He, J.B. / Wei, W. / Pan, H.X. / Wang, X. / Yang, S. / Liang, Y. / Tang, G.L. / Zhou, J.

History

Deposition	Dec 18, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 28, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8xhp.cif.gz	222.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8xhp.ent.gz	142.5 KB	Display	PDB format
PDBx/mmJSON format	8xhp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8xhp_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	8xhp_full_validation.pdf.gz	1.3 MB	Display
Data in XML	8xhp_validation.xml.gz	41.3 KB	Display
Data in CIF	8xhp_validation.cif.gz	55 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xh/8xhp ftp://data.pdbj.org/pub/pdb/validation_reports/xh/8xhp	HTTPS FTP

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Related structure data

Related structure data	8xhqC 8xhtC 8xhxC 8xhyC 7v3oS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

Deposited unit

A: Fe/2OG dependent dioxygenase

B: Fe/2OG dependent dioxygenase

C: Fe/2OG dependent dioxygenase

hetero molecules

106 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fe/2OG dependent dioxygenase

hetero molecules

defined by author
Evidence: gel filtration
35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fe/2OG dependent dioxygenase

hetero molecules

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

3

C: Fe/2OG dependent dioxygenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	128.966, 74.233, 98.046
Angle α, β, γ (deg.)	90.000, 104.134, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Fe/2OG dependent dioxygenase Mass: 34952.859 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₆O₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 51.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES/imidazole pH6.5, 0.03 M of each divalent cation (0.3 M magnesium chloride, 0.3 M calcium chloride) and 10% PEG20000, 20%PEG MME 550

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.86→19.772 Å / Num. obs: 75346 / % possible obs: 99.9 % / Redundancy: 6.1 % / B_iso Wilson estimate: 25.9139882543 Å² / CC_1/2: 0.987 / R_merge(I) obs: 0.163 / R_pim(I) all: 0.072 / Net I/σ(I): 6.3
Reflection shell	Resolution: 1.86→1.9 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.767 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4444 / CC_1/2: 0.682 / R_pim(I) all: 0.324 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS	Version February 5, 2021	data reduction
XDS	Version February 5, 2021	data scaling
PHASER	1.11.1_2575	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7V3O

7v3o

Resolution: 1.86000825296→19.7719294685 Å / SU ML: 0.220775477724 / Cross valid method: FREE R-VALUE / σ(F): 1.33784582786 / Phase error: 23.2818922412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.231614889352	3849	5.10904336515 %
R_work	0.2053938082	71488	-
obs	0.206766130415	75337	99.9761130648 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.0913021028 Å²

Refinement step

Cycle: LAST / Resolution: 1.86000825296→19.7719294685 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6390	0	45	471	6906

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00352260714168	6604
X-RAY DIFFRACTION	f_angle_d	0.706006114364	8957
X-RAY DIFFRACTION	f_chiral_restr	0.0451544150874	937
X-RAY DIFFRACTION	f_plane_restr	0.0042753643757	1217
X-RAY DIFFRACTION	f_dihedral_angle_d	19.5432854314	3871

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8600083-1.8835	0.306057605641	132	0.274828486437	2590	X-RAY DIFFRACTION	100
1.8835-1.9083	0.337972711263	147	0.265174663405	2661	X-RAY DIFFRACTION	99.9288256228
1.9083-1.9344	0.313835376111	137	0.254526881697	2582	X-RAY DIFFRACTION	100
1.9344-1.962	0.244944324927	151	0.242482890979	2678	X-RAY DIFFRACTION	100
1.962-1.9913	0.268602493144	147	0.234229626864	2605	X-RAY DIFFRACTION	99.9636759898
1.9913-2.0224	0.263874881498	133	0.230701424035	2649	X-RAY DIFFRACTION	100
2.0224-2.0555	0.250257030397	134	0.220747074834	2645	X-RAY DIFFRACTION	100
2.0555-2.0909	0.248926184549	153	0.21133291051	2621	X-RAY DIFFRACTION	100
2.0909-2.1289	0.233532410689	129	0.205525529413	2657	X-RAY DIFFRACTION	100
2.1289-2.1698	0.248298370589	142	0.212750678077	2636	X-RAY DIFFRACTION	100
2.1698-2.214	0.262539773652	134	0.209099485085	2648	X-RAY DIFFRACTION	100
2.214-2.2621	0.237606989224	123	0.196758527959	2664	X-RAY DIFFRACTION	100
2.2621-2.3146	0.261273808956	145	0.205654018401	2669	X-RAY DIFFRACTION	100
2.3146-2.3724	0.226586049583	135	0.211138211984	2611	X-RAY DIFFRACTION	100
2.3724-2.4365	0.229890842366	119	0.20236055806	2668	X-RAY DIFFRACTION	99.9641319943
2.4365-2.508	0.253171375498	150	0.215303678229	2637	X-RAY DIFFRACTION	100
2.508-2.5888	0.245332954003	135	0.217962007668	2644	X-RAY DIFFRACTION	100
2.5888-2.6811	0.278731327944	157	0.221216420782	2644	X-RAY DIFFRACTION	100
2.6811-2.7882	0.251443277678	122	0.215690839642	2649	X-RAY DIFFRACTION	100
2.7882-2.9147	0.296899811843	133	0.22129614688	2682	X-RAY DIFFRACTION	99.9290024849
2.9147-3.0678	0.226170858691	136	0.210662826524	2682	X-RAY DIFFRACTION	99.9645264278
3.0678-3.2592	0.185116092864	152	0.200436426796	2620	X-RAY DIFFRACTION	99.9279019466
3.2592-3.5096	0.219674547743	141	0.197060262958	2669	X-RAY DIFFRACTION	100
3.5096-3.8604	0.20498696115	155	0.185848632595	2656	X-RAY DIFFRACTION	100
3.8604-4.4136	0.201061086169	138	0.18349159981	2685	X-RAY DIFFRACTION	100
4.4136-5.5403	0.20474726097	204	0.189546691697	2609	X-RAY DIFFRACTION	99.9644633973
5.5403-19.7719	0.238370279018	165	0.201203467972	2727	X-RAY DIFFRACTION	99.8274076631

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