PDB-2vl6: STRUCTURAL ANALYSIS OF THE SULFOLOBUS SOLFATARICUS MCM PROTEIN N-...

ID or keywords:

Entry

Database: PDB / ID: 2vl6

Title

STRUCTURAL ANALYSIS OF THE SULFOLOBUS SOLFATARICUS MCM PROTEIN N- TERMINAL DOMAIN

Components

MINICHROMOSOME MAINTENANCE PROTEIN MCM

Keywords

DNA BINDING PROTEIN / MCM / HELICASE / HYDROLASE / ZINC-FINGER / ATP-BINDING / DNA-BINDING / SSDNA BINDING / DNA REPLICATION / NUCLEOTIDE-BINDING

Function / homology

Function and homology information

single-stranded 3'-5' DNA helicase activity / MCM complex / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / single-stranded DNA binding / DNA helicase / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function

Biological species

SULFOLOBUS SOLFATARICUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Liu, W. / Pucci, B. / Rossi, M. / Pisani, F.M. / Ladenstein, R.

Citation

Journal: Nucleic Acids Res. / Year: 2008
Title: Structural Analysis of the Sulfolobus Solfataricus Mcm Protein N-Terminal Domain.
Authors: Liu, W. / Pucci, B. / Rossi, M. / Pisani, F.M. / Ladenstein, R.

History

Deposition	Jan 8, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 4, 2013	Group: Derived calculations / Other / Source and taxonomy
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vl6.cif.gz	165.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2vl6.ent.gz	132 KB	Display	PDB format
PDBx/mmJSON format	2vl6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2vl6_validation.pdf.gz	452.3 KB	Display	wwPDB validaton report
Full document	2vl6_full_validation.pdf.gz	484.7 KB	Display
Data in XML	2vl6_validation.xml.gz	31.6 KB	Display
Data in CIF	2vl6_validation.cif.gz	42.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vl/2vl6 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vl6	HTTPS FTP

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Related structure data

Related structure data	1ltlS S: Starting model for refinement
Similar structure data	4pog-1 4pog-2 5iy0-d 4pof-d 4lk3-d 5mux-d 6733 20805 Search similar-shape structures by Omokage search (details) 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	#168 - Dec 2013 DNA Helicase similarity (11)

Deposited unit

A: MINICHROMOSOME MAINTENANCE PROTEIN MCM

B: MINICHROMOSOME MAINTENANCE PROTEIN MCM

C: MINICHROMOSOME MAINTENANCE PROTEIN MCM

hetero molecules

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

1

A: MINICHROMOSOME MAINTENANCE PROTEIN MCM

B: MINICHROMOSOME MAINTENANCE PROTEIN MCM

C: MINICHROMOSOME MAINTENANCE PROTEIN MCM

hetero molecules

A: MINICHROMOSOME MAINTENANCE PROTEIN MCM

B: MINICHROMOSOME MAINTENANCE PROTEIN MCM

C: MINICHROMOSOME MAINTENANCE PROTEIN MCM

hetero molecules

defined by author&software
187 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	193.994, 52.236, 115.574
Angle α, β, γ (deg.)	90.00, 124.15, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	A
2	2	B
3	2	C

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	GLN	GLN	VAL	VAL	1	A	A	7 - 96	7 - 96
2	1	GLN	GLN	VAL	VAL	1	B	B	7 - 96	7 - 96
3	1	GLN	GLN	VAL	VAL	1	C	C	7 - 96	7 - 96
1	2	HIS	HIS	SER	SER	2	A	A	97 - 265	97 - 265
2	2	HIS	HIS	SER	SER	2	B	B	97 - 265	97 - 265
3	2	HIS	HIS	SER	SER	2	C	C	97 - 265	97 - 265

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.558123, -0.027933, 0.829288), (0.00676, 0.999553, 0.029119), (-0.829731, -0.010646, 0.558062)	2.225, -0.47, 0.209
2	given	(0.463548, -0.012719, -0.885981), (0.028614, 0.99959, 0.000621), (0.88561, -0.025639, 0.463722)	1.491, -0.525, -1.112

#1: Protein	MINICHROMOSOME MAINTENANCE PROTEIN MCM / SSO MCM N-TER Mass: 31143.121 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-29A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9UXG1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.6 % / Description: NONE
Crystal grow	pH: 5.5 Details: 20% PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.1 M SODIUM ACETATE, PH 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
Detector	Type: MARRESEARCH / Detector: CCD / Date: Aug 26, 2006 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2.8→31.9 Å / Num. obs: 24102 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 18.38 % / R_merge(I) obs: 0.06 / Net I/σ(I): 21.07
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 4.35 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTL

1ltl

Resolution: 2.8→31.88 Å / Cor.coef. F_o:F_c: 0.924 / Cor.coef. F_o:F_c free: 0.894 / SU B: 38.201 / SU ML: 0.353 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMODELING OF RESIDUES 7-189 IS NEEDED AFTER MOLECULAR REPLACEMENT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.283	1226	5.1 %	RANDOM
R_work	0.233	-	-	-
obs	0.236	22821	100 %	-

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 mean: 34.84 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	-0.18 Å²
2-	-	-0.21 Å²	0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→31.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6348	0	3	38	6389

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	6471
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.771	1.987	8757
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.032	5	774
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.924	24.554	303
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.56	15	1251
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.049	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	999
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4800
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.264	0.2	3024
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.332	0.2	4518
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.2	0.2	239
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.402	0.2	93
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.247	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.482	1.5	4006
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.816	2	6429
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.542	3	2734
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.599	4.5	2328
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	758	tight positional	0.06	0.05
1	2	B	758	tight positional	0.04	0.05
1	3	C	758	tight positional	0.04	0.05
2	1	A	676	tight positional	0.08	0.05
2	2	B	676	tight positional	0.08	0.05
2	3	C	676	tight positional	0.07	0.05
2	1	A	683	medium positional	0.3	0.5
2	2	B	683	medium positional	0.33	0.5
2	3	C	683	medium positional	0.3	0.5
1	1	A	758	tight thermal	0.09	0.5
1	2	B	758	tight thermal	0.06	0.5
1	3	C	758	tight thermal	0.07	0.5
2	1	A	676	tight thermal	0.1	0.5
2	2	B	676	tight thermal	0.11	0.5
2	3	C	676	tight thermal	0.11	0.5
2	1	A	683	medium thermal	0.75	2
2	2	B	683	medium thermal	0.71	2
2	3	C	683	medium thermal	0.65	2

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.485	92
R_work	0.396	1683

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	11.9689	-0.826	-0.7709	8.8152	2.6403	5.9902	-0.0567	-1.299	0.6425	1.2074	-0.1909	-0.0186	0.1545	-0.3158	0.2477	0.1972	-0.0536	-0.07	0.1571	-0.0976	-0.0143	9.9552	-3.3051	51.2624
2	6.5892	1.9973	4.6	4.9968	2.2436	5.3799	-0.2453	-0.2047	0.3674	0.1027	0.1127	-0.4059	-0.3289	0.085	0.1327	-0.0367	0.0408	-0.0053	-0.0393	0.0095	-0.0357	7.7966	-4.4011	39.911
3	1.967	2.9058	-0.6714	29.1105	-8.7147	2.9618	-0.2822	-0.0488	0.7952	-0.3068	0.317	0.0538	-0.4002	-0.2232	-0.0348	0.1789	0.0029	-0.0027	-0.0228	-0.0705	0.0955	15.1044	7.7638	19.0393
4	12.441	2.6618	0.5208	5.2535	2.3774	4.2931	-0.2428	0.3441	-0.0523	-0.7285	0.0891	0.3429	-0.0529	-0.1322	0.1537	-0.0434	-0.0386	-0.0303	-0.1459	-0.0534	-0.1427	0.5903	-12.5547	27.9823
5	17.4838	2.5437	2.4704	7.1867	4.9666	13.2798	-0.0286	-2.5153	0.6375	0.4968	-0.9882	1.1843	-0.3077	-2.1517	1.0168	0.2035	-0.0279	0.1447	1.2686	-0.331	0.2737	-38.0063	-3.6085	34.819
6	5.2132	0.3828	0.3098	1.2271	-0.2069	9.8185	-0.1019	-1.4056	0.4829	0.0937	-0.3691	-0.0606	-0.684	-0.9046	0.471	0.0095	0.0541	0.0097	0.4646	-0.0448	0.0706	-29.8373	-4.6021	26.6554
7	5.2936	10.2971	0.0213	28.5863	-1.5668	1.1187	-0.2154	0.0211	0.3209	-0.3684	0.2401	-0.0778	-0.8588	-0.3394	-0.0248	0.2559	0.1246	-0.0628	0.0603	-0.0003	0.1241	-8.4833	7.7832	21.3546
8	3.4327	-2.2484	3.062	8.0654	2.3518	9.7714	0.1117	-0.0472	-0.2791	-0.7513	-0.2543	-0.7023	-0.4244	-0.2632	0.1426	-0.139	0.0098	0.0702	0.028	-0.0043	0.0144	-24.0849	-12.3504	13.8282
9	10.895	2.2624	-0.2526	11.047	-4.2964	12.558	0.368	-1.5184	0.0488	1.062	-1.5413	-3.1433	-1.0761	2.2464	1.1734	0.2646	-0.4303	-0.2376	0.835	0.5	1.3354	50.3385	-4.5345	17.0151
10	5.9256	0.2249	-1.3446	4.8525	-0.9746	5.0987	0.0338	0.0832	0.4747	-0.3833	-0.5544	-1.5237	-0.6193	1.3677	0.5206	0.1236	-0.1832	0.0321	0.3041	0.2353	0.4439	39.5454	-5.0321	13.423
11	1.8942	-6.9176	1.5019	32.0554	-11.2059	6.0094	0.074	-0.1119	0.3579	0.0902	0.2452	0.6084	-0.6108	0.0055	-0.3193	0.1421	-0.059	0.0093	0.0845	-0.0731	0.0497	23.8687	7.77	-2.7522
12	8.0823	1.8635	-4.6495	8.0656	0.0833	8.0653	0.1542	0.1103	-0.005	-0.1137	-0.2753	0.2836	-0.1697	-0.0305	0.1211	-0.1092	-0.0877	-0.0391	-0.0992	0.0202	-0.2066	25.0541	-12.606	14.2051

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 68
2	X-RAY DIFFRACTION	2	A	69 - 128
3	X-RAY DIFFRACTION	3	A	129 - 194
4	X-RAY DIFFRACTION	4	A	195 - 265
5	X-RAY DIFFRACTION	5	B	7 - 68
6	X-RAY DIFFRACTION	6	B	69 - 128
7	X-RAY DIFFRACTION	7	B	129 - 194
8	X-RAY DIFFRACTION	8	B	195 - 265
9	X-RAY DIFFRACTION	9	C	7 - 68
10	X-RAY DIFFRACTION	10	C	69 - 128
11	X-RAY DIFFRACTION	11	C	129 - 194
12	X-RAY DIFFRACTION	12	C	195 - 265

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