PDB-8fhb: Protein 32 with aldehyde deformylating oxidase activity from Syne...

ID or keywords:

Entry

Database: PDB / ID: 8fhb

Title

Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp.

Components

tRNA-(MS[2]IO[6]A)-hydroxylase

Keywords

LYASE / aldehyde deformylating oxygenase

Function / homology

tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity / tRNA-hydroxylase MiaE / tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) / tRNA modification / Ferritin-like / Ferritin-like superfamily / metal ion binding / : / tRNA-(MS[2]IO[6]A)-hydroxylase

Function and homology information

Biological species

Synechococcus sp. RCC307 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Arenas, R. / Wilson, D.K. / Mak, W.S. / Siegel, J.B.

Funding support

1items

Citation

Journal: To Be Published
Title: Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp.
Authors: Arenas, R. / Wilson, D.K. / Mak, W.S. / Siegel, J.B.

History

Deposition	Dec 13, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 20, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fhb.cif.gz	60.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8fhb.ent.gz	39.3 KB	Display	PDB format
PDBx/mmJSON format	8fhb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fhb_validation.pdf.gz	826.7 KB	Display	wwPDB validaton report
Full document	8fhb_full_validation.pdf.gz	827.1 KB	Display
Data in XML	8fhb_validation.xml.gz	10.3 KB	Display
Data in CIF	8fhb_validation.cif.gz	14 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fh/8fhb ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fhb	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (1) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: tRNA-(MS[2]IO[6]A)-hydroxylase

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	55.192, 74.330, 111.953
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	tRNA-(MS[2]IO[6]A)-hydroxylase Mass: 25780.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. RCC307 (bacteria) / Gene: miaE / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A5GR51
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.74 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4,000, 200 mM MgCl2, 100 mM HEPES HCl

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.95→37.32 Å / Num. obs: 17168 / % possible obs: 100 % / Redundancy: 13.2 % / B_iso Wilson estimate: 27.8 Å² / CC_1/2: 1 / R_merge(I) obs: 0.059 / R_pim(I) all: 0.017 / R_rim(I) all: 0.061 / Net I/σ(I): 26.7
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 13.7 % / R_merge(I) obs: 0.666 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1177 / CC_1/2: 0.937 / R_pim(I) all: 0.186 / R_rim(I) all: 0.692 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.95→37.165 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.95 / SU B: 3.465 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2167	826	4.818 %	0.05
R_work	0.1692	16317	-	-
all	0.172	-	-	-
obs	-	17143	99.901 %	-

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: 35.558 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.004 Å²	0 Å²	0 Å²
2-	-	0.018 Å²	0 Å²
3-	-	-	-0.022 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→37.165 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1614	0	1	85	1700

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	1651
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1531
X-RAY DIFFRACTION	r_angle_refined_deg	2.117	1.644	2244
X-RAY DIFFRACTION	r_angle_other_deg	0.727	1.553	3563
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.013	5	203
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.147	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.201	10	277
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.068	10	79
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	248
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	1914
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	322
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	355
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	1346
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	805
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	884
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	62
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.226	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.181	0.2	91
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.141	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	4.29	3.477	815
X-RAY DIFFRACTION	r_mcbond_other	4.288	3.477	815
X-RAY DIFFRACTION	r_mcangle_it	5.571	5.192	1017
X-RAY DIFFRACTION	r_mcangle_other	5.569	5.196	1018
X-RAY DIFFRACTION	r_scbond_it	5.778	4.058	836
X-RAY DIFFRACTION	r_scbond_other	5.774	4.062	837
X-RAY DIFFRACTION	r_scangle_it	7.761	5.863	1227
X-RAY DIFFRACTION	r_scangle_other	7.758	5.867	1228
X-RAY DIFFRACTION	r_lrange_it	8.901	45.142	1852
X-RAY DIFFRACTION	r_lrange_other	8.894	45.105	1847

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
1.95-2.001	0.256	69	0.252	1166	0.252	1236	0.941	0.951	99.9191	0.206
2.001-2.055	0.255	48	0.216	1158	0.218	1206	0.934	0.968	100	0.18
2.055-2.115	0.225	55	0.194	1150	0.195	1205	0.969	0.975	100	0.168
2.115-2.179	0.261	53	0.181	1071	0.184	1125	0.958	0.98	99.9111	0.152
2.179-2.251	0.234	53	0.172	1061	0.175	1116	0.966	0.982	99.8208	0.145
2.251-2.329	0.204	46	0.173	1060	0.175	1108	0.974	0.981	99.8195	0.156
2.329-2.417	0.256	54	0.163	974	0.168	1028	0.962	0.983	100	0.142
2.417-2.515	0.213	41	0.171	967	0.172	1009	0.968	0.982	99.9009	0.151
2.515-2.627	0.232	46	0.158	921	0.161	967	0.974	0.986	100	0.14
2.627-2.754	0.219	43	0.175	889	0.177	935	0.974	0.983	99.6791	0.157
2.754-2.902	0.305	41	0.186	845	0.192	886	0.955	0.979	100	0.17
2.902-3.077	0.214	51	0.199	785	0.2	836	0.971	0.974	100	0.184
3.077-3.288	0.25	42	0.186	750	0.189	792	0.961	0.979	100	0.176
3.288-3.549	0.236	30	0.161	712	0.163	743	0.963	0.985	99.8654	0.158
3.549-3.884	0.194	33	0.153	651	0.155	685	0.973	0.988	99.854	0.153
3.884-4.337	0.192	31	0.143	587	0.145	618	0.983	0.988	100	0.145
4.337-4.996	0.203	33	0.143	525	0.147	558	0.976	0.989	100	0.147
4.996-6.092	0.182	24	0.191	454	0.19	479	0.989	0.984	99.7912	0.195
6.092-8.501	0.173	17	0.138	362	0.14	380	0.987	0.986	99.7368	0.14
8.501-37.165	0.178	16	0.17	229	0.171	245	0.964	0.98	100	0.198

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