PDB-8fhc: Protein 41 with aldehyde deformylating oxidase activity from Gamm...

ID or keywords:

Entry

Database: PDB / ID: 8fhc

Title

Protein 41 with aldehyde deformylating oxidase activity from Gamma proteobacterium

Components

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

Keywords

LYASE

Function / homology

Function and homology information

tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity / tRNA modification / metal ion binding
Similarity search - Function

Biological species

gamma proteobacterium HdN1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.097 Å

Authors

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

Funding support

1items

Citation

Journal: To Be Published
Title: Protein 41 with aldehyde deformylating oxidase activity from Gamma proteobacterium
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	8fhc.cif.gz	110.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8fhc.ent.gz	78.7 KB	Display	PDB format
PDBx/mmJSON format	8fhc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fhc_validation.pdf.gz	6.4 MB	Display	wwPDB validaton report
Full document	8fhc_full_validation.pdf.gz	6.5 MB	Display
Data in XML	8fhc_validation.xml.gz	19.3 KB	Display
Data in CIF	8fhc_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fh/8fhc ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fhc	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) #122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

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

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

hetero molecules

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

1

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

hetero molecules

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

2

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.296, 85.711, 112.558
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	tRNA-(MS[2]IO[6]A)-hydroxylase Mass: 25948.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) gamma proteobacterium HdN1 (bacteria) / Gene: miaE, HDN1F_16480 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E1VK89
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CHD / CHOLIC ACID Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₄₀O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 27% PEG 3350, 200 mM NaCl, 1.5 mM cholalic acid sodium salt, 100 mM imidazole PH range: 7

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Data collection

Diffraction	Mean temperature: 100 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: Aug 17, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.097→39.443 Å / Num. obs: 28065 / % possible obs: 99.6 % / Redundancy: 9.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.107 / R_pim(I) all: 0.035 / R_rim(I) all: 0.113 / Net I/σ(I): 16
Reflection shell	Resolution: 2.1→2.16 Å / Redundancy: 9.2 % / R_merge(I) obs: 0.579 / Num. unique obs: 2195 / CC_1/2: 0.926 / R_pim(I) all: 0.198 / R_rim(I) all: 0.614

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.097→39.443 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.926 / SU B: 5.505 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.236 / ESU R Free: 0.189
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2362	1384	4.941 %	0.05
R_work	0.1954	26624	-	-
all	0.197	-	-	-
obs	-	28008	99.46 %	-

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: 25.821 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.088 Å²	0 Å²	-0 Å²
2-	-	2.935 Å²	-0 Å²
3-	-	-	0.153 Å²

Refinement step

Cycle: LAST / Resolution: 2.097→39.443 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3486	0	45	198	3729

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	3592
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3264
X-RAY DIFFRACTION	r_angle_refined_deg	1.356	1.655	4869
X-RAY DIFFRACTION	r_angle_other_deg	0.444	1.552	7620
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.104	5	426
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.302	5	34
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.069	10	624
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.227	10	186
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	541
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4094
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	726
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	841
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	3072
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1802
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1885
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	191
X-RAY DIFFRACTION	r_metal_ion_refined	0.037	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.206	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.099	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	1.812	2.597	1710
X-RAY DIFFRACTION	r_mcbond_other	1.81	2.597	1710
X-RAY DIFFRACTION	r_mcangle_it	2.671	3.884	2134
X-RAY DIFFRACTION	r_mcangle_other	2.671	3.886	2135
X-RAY DIFFRACTION	r_scbond_it	2.909	2.914	1882
X-RAY DIFFRACTION	r_scbond_other	2.909	2.914	1881
X-RAY DIFFRACTION	r_scangle_it	4.488	4.258	2735
X-RAY DIFFRACTION	r_scangle_other	4.488	4.258	2736
X-RAY DIFFRACTION	r_lrange_it	5.829	36.131	4217
X-RAY DIFFRACTION	r_lrange_other	5.739	35.708	4192

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
2.097-2.151	0.29	98	0.25	1868	0.252	2033	0.931	0.948	96.7044	0.231
2.151-2.21	0.284	96	0.222	1885	0.225	1995	0.905	0.959	99.2982	0.196
2.21-2.273	0.265	109	0.211	1831	0.214	1940	0.921	0.968	100	0.186
2.273-2.343	0.23	105	0.195	1772	0.197	1879	0.962	0.97	99.8936	0.167
2.343-2.42	0.31	71	0.194	1742	0.198	1822	0.952	0.971	99.506	0.169
2.42-2.504	0.243	98	0.192	1682	0.195	1780	0.931	0.967	100	0.158
2.504-2.598	0.243	93	0.188	1617	0.191	1712	0.958	0.972	99.8832	0.152
2.598-2.704	0.215	70	0.195	1585	0.196	1656	0.961	0.972	99.9396	0.163
2.704-2.824	0.333	78	0.216	1495	0.222	1587	0.932	0.968	99.1178	0.177
2.824-2.961	0.246	66	0.2	1448	0.202	1514	0.959	0.974	100	0.165
2.961-3.12	0.244	76	0.207	1373	0.209	1451	0.952	0.972	99.8622	0.18
3.12-3.308	0.256	77	0.219	1305	0.221	1383	0.957	0.969	99.9277	0.193
3.308-3.535	0.201	59	0.2	1237	0.201	1296	0.974	0.976	100	0.184
3.535-3.815	0.207	65	0.185	1154	0.186	1219	0.971	0.98	100	0.173
3.815-4.175	0.189	59	0.164	1042	0.166	1120	0.977	0.984	98.3036	0.152
4.175-4.662	0.192	51	0.158	980	0.16	1031	0.978	0.987	100	0.155
4.662-5.37	0.198	45	0.184	882	0.185	927	0.974	0.983	100	0.174
5.37-6.547	0.279	35	0.21	744	0.213	779	0.973	0.98	100	0.199
6.547-9.134	0.207	21	0.163	591	0.165	626	0.981	0.983	97.7636	0.165
9.134-39.443	0.24	12	0.215	391	0.216	403	0.971	0.97	100	0.222

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