PDB-8k41: mercuric reductase,GbsMerA, - FAD bound

ID or keywords:

Entry

Database: PDB / ID: 8k41

Title

mercuric reductase,GbsMerA, - FAD bound

Components

NAD(P)/FAD-dependent oxidoreductase

Keywords

TRANSFERASE / Mercuric reductase / Gelidibacter salicanalis PAMC21136 / Hg resistance / Heavy metal detoxification

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Gelidibacter salicanalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.39 Å

Authors

Do, H.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Sci Rep / Year: 2023
Title: Biochemical and structural basis of mercuric reductase, GbsMerA, from Gelidibacter salicanalis PAMC21136.
Authors: Pardhe, B.D. / Lee, M.J. / Lee, J.H. / Do, H. / Oh, T.J.

History

Deposition	Jul 17, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8k41.cif.gz	109.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8k41.ent.gz	77.5 KB	Display	PDB format
PDBx/mmJSON format	8k41.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8k41_validation.pdf.gz	993 KB	Display	wwPDB validaton report
Full document	8k41_full_validation.pdf.gz	996.1 KB	Display
Data in XML	8k41_validation.xml.gz	17.7 KB	Display
Data in CIF	8k41_validation.cif.gz	23.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k4/8k41 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/8k41	HTTPS FTP

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Related structure data

Related structure data	8k40C C: citing same article (ref.)
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	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (6) #154 - Oct 2012 Citric Acid Cycle similarity (6) #82 - Oct 2006 Cytochrome p450 similarity (2) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: NAD(P)/FAD-dependent oxidoreductase

hetero molecules

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

1

A: NAD(P)/FAD-dependent oxidoreductase

hetero molecules

A: NAD(P)/FAD-dependent oxidoreductase

hetero molecules

defined by author&software
Evidence: gel filtration
103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.330, 102.330, 108.700
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	NAD(P)/FAD-dependent oxidoreductase Mass: 49953.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gelidibacter salicanalis (bacteria) / Gene: JEM65_00875 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A934NG65
#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 3.29 Å³/Da / Density % sol: 62.6 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.12M of ethylene glycol, 0.1M bicine/Trizma pH8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 12, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.39→29.57 Å / Num. obs: 26169 / % possible obs: 99 % / Redundancy: 20.1 % / CC_1/2: 1 / Net I/σ(I): 27.8
Reflection shell	Resolution: 2.39→2.48 Å / Num. unique obs: 2695 / CC_1/2: 0.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.39→29.57 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.912 / SU B: 9.268 / SU ML: 0.211 / Cross valid method: FREE R-VALUE / ESU R: 0.296 / ESU R Free: 0.25
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2711	1295	4.949 %
R_work	0.209	24874	-
all	0.212	-	-
obs	-	26169	98.676 %

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: 53.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.006 Å²	0.003 Å²	0 Å²
2-	-	0.006 Å²	-0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.39→29.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3448	0	101	13	3562

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	3628
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3412
X-RAY DIFFRACTION	r_angle_refined_deg	1.573	1.649	4921
X-RAY DIFFRACTION	r_angle_other_deg	1.171	1.579	7948
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.915	5	446
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.447	23.548	155
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.323	15	632
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.507	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	498
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3973
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	698
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	713
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	3081
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	1707
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1625
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.087	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.125	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.237	0.2	56
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.069	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	4.139	5.511	1787
X-RAY DIFFRACTION	r_mcbond_other	4.134	5.51	1786
X-RAY DIFFRACTION	r_mcangle_it	5.617	8.273	2232
X-RAY DIFFRACTION	r_mcangle_other	5.617	8.274	2233
X-RAY DIFFRACTION	r_scbond_it	4.184	5.943	1840
X-RAY DIFFRACTION	r_scbond_other	4.185	5.945	1837
X-RAY DIFFRACTION	r_scangle_it	6.171	8.712	2688
X-RAY DIFFRACTION	r_scangle_other	6.169	8.711	2689
X-RAY DIFFRACTION	r_lrange_it	7.856	63.63	3865
X-RAY DIFFRACTION	r_lrange_other	7.855	63.626	3866

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 (%)
2.39-2.452	0.397	94	0.323	1785	X-RAY DIFFRACTION	97.8646
2.452-2.519	0.356	93	0.296	1744	X-RAY DIFFRACTION	97.8689
2.519-2.592	0.317	75	0.276	1730	X-RAY DIFFRACTION	98.1512
2.592-2.672	0.324	87	0.268	1688	X-RAY DIFFRACTION	98.8307
2.672-2.759	0.361	100	0.267	1613	X-RAY DIFFRACTION	98.903
2.759-2.856	0.28	66	0.248	1576	X-RAY DIFFRACTION	98.2057
2.856-2.964	0.282	59	0.216	1527	X-RAY DIFFRACTION	98.9395
2.964-3.085	0.351	102	0.231	1445	X-RAY DIFFRACTION	98.9763
3.085-3.222	0.272	85	0.235	1394	X-RAY DIFFRACTION	98.7976
3.222-3.379	0.322	80	0.222	1348	X-RAY DIFFRACTION	99.2356
3.379-3.561	0.23	63	0.213	1296	X-RAY DIFFRACTION	98.8364
3.561-3.777	0.252	76	0.196	1204	X-RAY DIFFRACTION	98.9181
3.777-4.037	0.254	66	0.201	1148	X-RAY DIFFRACTION	99.102
4.037-4.36	0.269	57	0.171	1081	X-RAY DIFFRACTION	99.3886
4.36-4.775	0.201	46	0.151	995	X-RAY DIFFRACTION	99.6172
4.775-5.337	0.245	45	0.176	928	X-RAY DIFFRACTION	99.5906
5.337-6.158	0.309	26	0.216	812	X-RAY DIFFRACTION	99.1716
6.158-7.533	0.361	21	0.2	716	X-RAY DIFFRACTION	99.4602
7.533-10.616	0.204	38	0.143	533	X-RAY DIFFRACTION	98.6183
10.616-29.57	0.142	16	0.256	311	X-RAY DIFFRACTION	91.8539

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