PDB-3g3c: Mth0212 (WT) in complex with a 6bp dsDNA containing a single one ...

ID or keywords:

Entry

Database: PDB / ID: 3g3c

Title

Mth0212 (WT) in complex with a 6bp dsDNA containing a single one nucleotide long 3'-overhang

Components

5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3'
5'-D(*CP*GP*TP*AP*CP*TP*AP*CP*G)-3'
Exodeoxyribonuclease

Keywords

HYDROLASE/DNA / protein-DNA complex / HYDROLASE-DNA COMPLEX

Function / homology

Function and homology information

double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / endonuclease activity / DNA binding / metal ion binding
Similarity search - Function

Biological species

Methanothermobacter thermautotrophicus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.04 Å

Authors

Lakomek, K. / Dickmanns, A. / Ficner, R.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
Authors: Lakomek, K. / Dickmanns, A. / Ciirdaeva, E. / Schomacher, L. / Ficner, R.

History

Deposition	Feb 2, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 12, 2014	Group: Derived calculations
Revision 1.3	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.4	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3g3c.cif.gz	130 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g3/3g3c ftp://data.pdbj.org/pub/pdb/validation_reports/g3/3g3c	HTTPS FTP

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Related structure data

Related structure data	3fziSC 3g00C 3g0aC 3g0rC 3g1kC 3g2cC 3g2dC 3g38C 3g3yC 3g4tC 3g8vC 3g91C 3ga6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3g4t-d 3jz1-1 4kyv-d 6gwe-d 4jnc-1 1zvk-d 4zy3-d 6vix-d 5yll-d 3wq7-d Search similar-shape structures by Omokage search (details) 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	#18 - Jun 2001 Myosin similarity (3) #19 - Jul 2001 Actin similarity (3) #91 - Jul 2007 Thymine Dimers similarity (1)

Deposited unit

A: Exodeoxyribonuclease

B: Exodeoxyribonuclease

H: 5'-D(*CP*GP*TP*AP*CP*TP*AP*CP*G)-3'

I: 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3'

hetero molecules

68.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	100.354, 79.337, 98.550
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	PHE	PHE	1	A	A	8 - 22	8 - 22
2	1	SER	SER	PHE	PHE	1	B	B	8 - 22	8 - 22
1	2	ALA	ALA	ALA	ALA	1	A	A	41 - 42	41 - 42
2	2	ALA	ALA	ALA	ALA	1	B	B	41 - 42	41 - 42
1	3	GLN	GLN	ARG	ARG	1	A	A	45 - 51	45 - 51
2	3	GLN	GLN	ARG	ARG	1	B	B	45 - 51	45 - 51
1	4	VAL	VAL	LYS	LYS	1	A	A	53 - 76	53 - 76
2	4	VAL	VAL	LYS	LYS	1	B	B	53 - 76	53 - 76
1	5	ARG	ARG	PHE	PHE	1	A	A	83 - 91	83 - 91
2	5	ARG	ARG	PHE	PHE	1	B	B	83 - 91	83 - 91
1	6	GLU	GLU	GLU	GLU	1	A	A	94 - 139	94 - 139
2	6	GLU	GLU	GLU	GLU	1	B	B	94 - 139	94 - 139
1	7	ARG	ARG	LEU	LEU	1	A	A	144 - 174	144 - 174
2	7	ARG	ARG	LEU	LEU	1	B	B	144 - 174	144 - 174
1	8	GLU	GLU	ASP	ASP	1	A	A	177 - 199	177 - 199
2	8	GLU	GLU	ASP	ASP	1	B	B	177 - 199	177 - 199
1	9	GLY	GLY	ILE	ILE	1	A	A	201 - 255	201 - 255
2	9	GLY	GLY	ILE	ILE	1	B	B	201 - 255	201 - 255
1	10	ALA	ALA	ILE	ILE	5	A	A	2 - 7	2 - 7
2	10	ALA	ALA	ILE	ILE	5	B	B	2 - 7	2 - 7
1	11	LEU	LEU	LYS	LYS	5	A	A	23 - 24	23 - 24
2	11	LEU	LEU	LYS	LYS	5	B	B	23 - 24	23 - 24
1	12	LYS	LYS	LYS	LYS	5	A	A	40	40
2	12	LYS	LYS	LYS	LYS	5	B	B	40	40
1	13	HIS	HIS	HIS	HIS	5	A	A	52	52
2	13	HIS	HIS	HIS	HIS	5	B	B	52	52
1	14	ASP	ASP	THR	THR	5	A	A	92 - 93	92 - 93
2	14	ASP	ASP	THR	THR	5	B	B	92 - 93	92 - 93
1	15	MET	MET	ASP	ASP	6	A	A	27 - 32	27 - 32
2	15	MET	MET	ASP	ASP	6	B	B	27 - 32	27 - 32
1	16	PRO	PRO	GLU	GLU	6	A	A	43 - 44	43 - 44
2	16	PRO	PRO	GLU	GLU	6	B	B	43 - 44	43 - 44
1	17	VAL	VAL	LEU	LEU	6	A	A	77 - 82	77 - 82
2	17	VAL	VAL	LEU	LEU	6	B	B	77 - 82	77 - 82
1	18	ARG	ARG	GLY	GLY	6	A	A	140 - 143	140 - 143
2	18	ARG	ARG	GLY	GLY	6	B	B	140 - 143	140 - 143
1	19	PRO	PRO	VAL	VAL	6	A	A	175 - 176	175 - 176
2	19	PRO	PRO	VAL	VAL	6	B	B	175 - 176	175 - 176
1	20	PRO	PRO	PRO	PRO	6	A	A	200	200
2	20	PRO	PRO	PRO	PRO	6	B	B	200	200
1	21	GLU	GLU	GLU	GLU	6	A	A	256	256
2	21	GLU	GLU	GLU	GLU	6	B	B	256	256

NCS ensembles :

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Protein , 1 types, 2 molecules AB

#1: Protein	Exodeoxyribonuclease / Mth0212 Mass: 31430.650 Da / Num. of mol.: 2 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: Delta H (DSM 1053) / Gene: mth0212, MTH212, MTH_212 / Plasmid: pET_B_001-mth212 (WT) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O26314, exodeoxyribonuclease III

#1: Protein

Exodeoxyribonuclease / Mth0212

Mass: 31430.650 Da / Num. of mol.: 2 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H (DSM 1053) / Gene: mth0212, MTH212, MTH_212 / Plasmid: pET_B_001-mth212 (WT) / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O26314, exodeoxyribonuclease III

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DNA chain , 2 types, 2 molecules HI

#2: DNA chain	5'-D(CPGPTPAPCPTPAPCPG)-3' Mass: 2715.799 Da / Num. of mol.: 1 / Source method*: obtained synthetically
#3: DNA chain	5'-D(CPGPTPAP(UPS)PTPAPCPG)-3' Mass: 2732.849 Da / Num. of mol.: 1 / Source method*: obtained synthetically

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Non-polymers , 4 types, 8 molecules

#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O

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Details

Compound details	THE 3'-END OF BOTH CHAINS(H AND I) ARE BOUND TO ROX 5/6 NHS MIXTURE (FLUORESCENCE DYE), WHICH IS ...THE 3'-END OF BOTH CHAINS(H AND I) ARE BOUND TO ROX 5/6 NHS MIXTURE (FLUORESCENCE DYE), WHICH IS NOT SHOWN IN THIS ENTRY.

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.87 Å³/Da / Density % sol: 57.17 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: reservoir: 40mM MgAc/50mM NaCac pH 6.0, 20% MPD; complex solution: 50mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, 1mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	KCl	1	1
2	KH2PO4/K2HPO4	1	1
3	MgCl2	1	1
4	H2O	1	1
5	MgAc	1	2
6	NaCac	1	2
7	MPD	1	2
8	H2O	1	2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 6, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 3.04→50 Å / Num. obs: 15706 / % possible obs: 100 % / Redundancy: 7.3 % / R_sym value: 0.082 / Net I/σ(I): 26.3
Reflection shell	Resolution: 3.04→3.15 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.1 / R_sym value: 0.509 / % possible all: 100

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
MAR345		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZI

3fzi

Resolution: 3.04→15 Å / Cor.coef. F_o:F_c: 0.924 / Cor.coef. F_o:F_c free: 0.877 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.766 / SU B: 23.158 / SU ML: 0.4 / SU R Cruickshank DPI: 1.407 / SU R_free: 0.518 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29432	773	5 %	RANDOM
R_work	0.23628	-	-	-
obs	0.23894	14742	99.63 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 104.24 Å² / B_iso mean: 72.524 Å² / B_iso min: 28.01 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.5 Å²	0 Å²	0 Å²
2-	-	-7.18 Å²	0 Å²
3-	-	-	5.68 Å²

Refinement step

Cycle: LAST / Resolution: 3.04→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4270	278	20	3	4571

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4711
X-RAY DIFFRACTION	r_angle_refined_deg	1.112	2.023	6410
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.95	5	510
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.615	22.75	240
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.357	15	760
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.65	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	645
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3580
X-RAY DIFFRACTION	r_mcbond_it	0.528	1.5	2544
X-RAY DIFFRACTION	r_mcangle_it	1.101	2	4100
X-RAY DIFFRACTION	r_scbond_it	1.179	3	2167
X-RAY DIFFRACTION	r_scangle_it	2.02	4.5	2310

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	123	tight positional	0.02	0.05
2	1	A	10	tight positional	0.01	0.05
3	1	A	63	tight positional	0.02	0.05
4	1	A	193	tight positional	0.02	0.05
5	1	A	77	tight positional	0.02	0.05
6	1	A	400	tight positional	0.04	0.05
7	1	A	244	tight positional	0.03	0.05
8	1	A	201	tight positional	0.02	0.05
9	1	A	473	tight positional	0.02	0.05
10	1	A	24	medium positional	0.14	0.5
11	1	A	8	medium positional	0.04	0.5
12	1	A	4	medium positional	0.03	0.5
13	1	A	4	medium positional	0.11	0.5
14	1	A	8	medium positional	0.04	0.5
10	2	B	21	loose positional	0.26	5
11	2	B	9	loose positional	1.41	5
12	2	B	5	loose positional	0.46	5
13	2	B	6	loose positional	1.85	5
14	2	B	7	loose positional	0.08	5
15	2	B	50	loose positional	0.99	5
16	2	B	16	loose positional	0.41	5
17	2	B	41	loose positional	0.44	5
18	2	B	29	loose positional	0.47	5
19	2	B	14	loose positional	0.18	5
20	2	B	7	loose positional	0.14	5
21	2	B	9	loose positional	0.4	5
1	1	A	123	tight thermal	0.04	0.5
2	1	A	10	tight thermal	0.04	0.5
3	1	A	63	tight thermal	0.03	0.5
4	1	A	193	tight thermal	0.04	0.5
5	1	A	77	tight thermal	0.04	0.5
6	1	A	400	tight thermal	0.03	0.5
7	1	A	244	tight thermal	0.03	0.5
8	1	A	201	tight thermal	0.04	0.5
9	1	A	473	tight thermal	0.04	0.5
10	1	A	24	medium thermal	0.26	2
11	1	A	8	medium thermal	0.79	2
12	1	A	4	medium thermal	0.66	2
13	1	A	4	medium thermal	0.14	2
14	1	A	8	medium thermal	0.05	2
10	2	B	21	loose thermal	0.33	10
11	2	B	9	loose thermal	0.39	10
12	2	B	5	loose thermal	0.43	10
13	2	B	6	loose thermal	0.32	10
14	2	B	7	loose thermal	0.24	10
15	2	B	50	loose thermal	3.51	10
16	2	B	16	loose thermal	0.36	10
17	2	B	41	loose thermal	1.15	10
18	2	B	29	loose thermal	0.32	10
19	2	B	14	loose thermal	0.4	10
20	2	B	7	loose thermal	0.3	10
21	2	B	9	loose thermal	1.73	10

LS refinement shell

Resolution: 3.038→3.114 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.376	55	-
R_work	0.341	1003	-
all	-	1058	-
obs	-	-	95.49 %

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