PDB-4pof: PfMCM N-terminal domain without DNA

ID or keywords:

Entry

Database: PDB / ID: 4pof

Title

PfMCM N-terminal domain without DNA

Components

Cell division control protein 21

Keywords

REPLICATION / DNA BINDING PROTEIN / OB-fold / DNA replication

Function / homology

Function and homology information

single-stranded 3'-5' DNA helicase activity / MCM complex / intein-mediated protein splicing / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / single-stranded DNA binding / endonuclease activity / DNA helicase / cell division / ATP binding / metal ion binding
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.648 Å

Authors

Froelich, C.A. / Kang, S. / Epling, L.B. / Bell, S.P. / Enemark, E.J.

Citation

Journal: Elife / Year: 2014
Title: A conserved MCM single-stranded DNA binding element is essential for replication initiation.
Authors: Froelich, C.A. / Kang, S. / Epling, L.B. / Bell, S.P. / Enemark, E.J.

History

Deposition	Feb 25, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 24, 2014	Group: Database references
Revision 1.2	Sep 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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	4pof.cif.gz	618 KB	Display	PDBx/mmCIF format
PDB format	pdb4pof.ent.gz	516.3 KB	Display	PDB format
PDBx/mmJSON format	4pof.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4pof_validation.pdf.gz	477.6 KB	Display	wwPDB validaton report
Full document	4pof_full_validation.pdf.gz	515.8 KB	Display
Data in XML	4pof_validation.xml.gz	55 KB	Display
Data in CIF	4pof_validation.cif.gz	72.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/po/4pof ftp://data.pdbj.org/pub/pdb/validation_reports/po/4pof	HTTPS FTP

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Related structure data

Related structure data	4pogC 1ltlS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5iy0-d 4pog-1 4pog-2 2vl6-1 6sko-d 6uge-d 20763 5wc0-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	#131 - Nov 2010 Inteins similarity (12) #219 - Mar 2018 Vacuolar ATPase similarity (12) #168 - Dec 2013 DNA Helicase similarity (11)

Deposited unit

A: Cell division control protein 21

B: Cell division control protein 21

C: Cell division control protein 21

D: Cell division control protein 21

E: Cell division control protein 21

F: Cell division control protein 21

hetero molecules

177 kDa, 6 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)	122.849, 103.064, 122.435
Angle α, β, γ (deg.)	90.00, 119.85, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 0 - 254 / Label seq-ID: 1 - 255

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F

#1: Protein	Cell division control protein 21 / MCM Mass: 29400.711 Da / Num. of mol.: 6 / Fragment: N-terminal domain (UNP residues 2-256) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: Cdc21, PF0482 / Plasmid: pRSFduet pLE009.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8U3I4
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

#1: Protein

Cell division control protein 21 / MCM

Mass: 29400.711 Da / Num. of mol.: 6 / Fragment: N-terminal domain (UNP residues 2-256)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: Cdc21, PF0482 / Plasmid: pRSFduet pLE009.3 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8U3I4

#2: Chemical

ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.81 Å³/Da / Density % sol: 67.72 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M sodium malonate, pH 7.0, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2009
Radiation	Monochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.648→50 Å / Num. all: 77156 / Num. obs: 76233 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / R_merge(I) obs: 0.1 / Net I/σ(I): 16.3
Reflection shell	Resolution: 2.648→2.74 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.569 / Mean I/σ(I) obs: 2.26 / Num. unique all: 7565 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
SERGUI		data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTL

1ltl

Resolution: 2.648→47.33 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.937 / SU B: 45.498 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26992	3839	5 %	RANDOM
R_work	0.25924	-	-	-
obs	0.25978	72376	98.6 %	-

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: 77.963 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.82 Å²	0 Å²	-3.38 Å²
2-	-	11.62 Å²	0 Å²
3-	-	-	-8.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.648→47.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12252	0	6	0	12258

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	12492
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.974	16866
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.525	5	1524
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.003	24.608	612
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.999	15	2334
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.267	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	1914
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	9372
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	2.203	1.5	7638
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	4.383	2	12492
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.678	3	4854
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	6.218	4.5	4374
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

Dom-ID: 1 / Ens-ID: 1 / Number: 2043 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	tight positional	0.03	0.05
B	tight positional	0.03	0.05
C	tight positional	0.03	0.05
D	tight positional	0.02	0.05
E	tight positional	0.03	0.05
F	tight positional	0.03	0.05
A	tight thermal	0.05	0.5
B	tight thermal	0.04	0.5
C	tight thermal	0.04	0.5
D	tight thermal	0.04	0.5
E	tight thermal	0.05	0.5
F	tight thermal	0.06	0.5

LS refinement shell

Resolution: 2.648→2.717 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.502	285	-
R_work	0.484	5183	-
obs	-	-	95.33 %

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	1.3902	0.344	1.4888	1.0269	0.0172	3.5669	0.012	-0.418	0.2178	-0.0758	-0.0359	0.0052	-0.0246	0.1482	0.0239	0.2302	0.0398	0.0349	0.3468	-0.0431	0.2924	10.8907	1.8345	28.8974
2	6.1654	-1.4085	0.5632	2.6837	-0.0756	0.3224	-0.0084	0.0022	-0.4446	-0.0359	0.0441	0.1605	0.1054	-0.2348	-0.0357	0.2948	-0.0153	0.0591	0.1479	-0.0022	0.2789	-2.6991	-10.6181	12.4113
3	3.4201	0.8121	1.2839	7.9626	-2.7078	1.8481	-0.2485	0.0206	1.1493	-0.1425	0.0193	-0.0246	-0.1599	-0.3529	0.2291	0.266	0.1302	0.0531	0.3101	0.0987	0.6691	10.8693	11.7133	0.8413
4	0.6149	0.0859	-0.8029	1.4241	-0.2462	4.8105	-0.0492	-0.2539	0.0212	-0.0564	0.004	-0.0067	0.0054	-0.7052	0.0452	0.1984	0.0223	0.0017	0.5906	0.0001	0.2441	-39.0825	1.2652	20.8171
5	2.4565	0.3305	2.021	1.5973	-1.0553	3.2378	-0.0111	0.2553	-0.352	-0.188	0.0863	-0.0654	0.5457	0.1007	-0.0752	0.3539	-0.0213	0.0522	0.281	-0.0641	0.3237	-31.4042	-11.1689	0.8667
6	1.4932	4.5898	0.8861	13.181	1.4418	2.5031	-0.3957	0.0822	-0.1504	-0.4627	0.0767	-0.4073	-0.655	-0.4289	0.319	0.3704	0.151	-0.0615	0.2057	-0.11	0.2751	-14.8925	11.3943	6.7733
7	5.1856	-0.0502	-1.1735	0.5458	0.3954	1.6463	0.0316	0.5997	0.0355	0.0119	0.0548	-0.1328	-0.2031	-0.6742	-0.0864	0.3018	-0.0034	0.0233	0.3964	-0.0006	0.2362	-56.9087	1.479	-26.3187
8	3.3534	1.1104	-3.6056	1.2098	-0.6867	4.9121	-0.1364	-0.1552	-0.3412	-0.03	0.0105	-0.133	0.4198	0.6841	0.1259	0.3468	0.0583	-0.0082	0.3327	-0.0766	0.3487	-35.9646	-11.2091	-29.7881
9	0.5711	2.5086	-0.3207	9.2576	2.7898	7.2028	0.1446	0.061	-0.1397	0.1408	0.1415	-0.1389	-0.9897	1.2838	-0.2861	0.3299	-0.2884	0.0194	0.7314	-0.0386	0.1533	-32.5677	10.975	-12.0995
10	3.0642	-0.2006	1.3069	0.6906	-0.1563	2.688	0.061	0.3851	0.1971	0.0773	-0.0809	0.0079	-0.0253	0.117	0.0199	0.2372	-0.0153	0.02	0.4117	-0.0031	0.2665	-25.1451	1.5609	-65.275
11	4.9664	0.413	0.2532	1.6667	0.5512	1.6629	-0.007	-0.137	-0.4423	0.1424	0.0817	-0.1635	0.1988	0.0379	-0.0747	0.2617	0.0094	0.0095	0.4805	0.0066	0.2895	-11.6029	-11.1352	-48.9361
12	5.2958	0.2407	-2.1766	10.4635	1.7329	2.2415	0.6845	-0.6012	1.4071	0.6407	-0.2026	0.4359	-0.5262	0.7035	-0.482	0.4254	-0.1401	0.212	0.4707	-0.0819	0.6013	-25.1121	11.092	-37.099
13	1.197	-0.1899	-0.1218	1.3391	-0.0901	4.5836	-0.0474	0.121	0.0062	0.0865	-0.0173	0.0161	-0.0906	0.1627	0.0647	0.1995	0.0084	0.0074	0.6857	0.0065	0.2183	24.6874	1.3196	-57.3149
14	1.806	0.1804	1.8517	1.2425	0.4211	5.0094	-0.0289	0.2445	-0.2027	0.1274	0.0337	0.0804	0.4321	-0.0742	-0.0048	0.2511	0.0256	0.0312	0.5734	0.0157	0.2562	17.284	-11.1193	-37.2639
15	5.4747	-0.056	2.922	7.9547	0.1602	2.2795	-0.6189	-0.5199	1.2485	-0.0933	0.0104	0.6139	-0.5866	-0.0937	0.6085	0.3158	0.0326	-0.1102	0.6306	-0.0849	0.555	0.3645	11.1147	-43.2641
16	4.1128	0.0335	-1.2177	0.7139	-0.8705	3.1218	0.0281	0.1886	0.0538	0.035	0.0219	0.0504	-0.1991	0.2077	-0.05	0.2323	-0.0147	0.0252	0.3749	0.0077	0.2377	42.6927	1.6714	-10.1915
17	1.4827	-0.5228	-1.2067	0.8608	0.2307	5.1256	-0.0193	0.3599	-0.0982	0.0344	0.0343	0.1053	0.2894	-0.1848	-0.0151	0.2974	-0.0073	0.0013	0.0974	-0.0086	0.3329	21.5313	-10.6168	-6.6033
18	2.4262	-1.5572	-0.2082	6.8395	-2.2801	5.0778	0.1165	-0.1578	0.2455	-0.1348	0.1023	0.0066	-1.1334	-0.8008	-0.2188	0.5454	0.0996	0.0384	0.2641	-0.0295	0.2322	18.5381	11.4027	-24.5681

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 100
2	X-RAY DIFFRACTION	2	A	101 - 127
3	X-RAY DIFFRACTION	2	A	183 - 254
4	X-RAY DIFFRACTION	3	A	128 - 182
5	X-RAY DIFFRACTION	3	A	301
6	X-RAY DIFFRACTION	4	B	0 - 100
7	X-RAY DIFFRACTION	5	B	101 - 127
8	X-RAY DIFFRACTION	5	B	183 - 254
9	X-RAY DIFFRACTION	6	B	128 - 182
10	X-RAY DIFFRACTION	6	B	301
11	X-RAY DIFFRACTION	7	C	0 - 100
12	X-RAY DIFFRACTION	8	C	101 - 127
13	X-RAY DIFFRACTION	8	C	183 - 254
14	X-RAY DIFFRACTION	9	C	128 - 182
15	X-RAY DIFFRACTION	9	C	301
16	X-RAY DIFFRACTION	10	D	0 - 100
17	X-RAY DIFFRACTION	11	D	101 - 127
18	X-RAY DIFFRACTION	11	D	183 - 254
19	X-RAY DIFFRACTION	12	D	128 - 182
20	X-RAY DIFFRACTION	12	D	301
21	X-RAY DIFFRACTION	13	E	0 - 100
22	X-RAY DIFFRACTION	14	E	101 - 127
23	X-RAY DIFFRACTION	14	E	183 - 254
24	X-RAY DIFFRACTION	15	E	128 - 182
25	X-RAY DIFFRACTION	15	E	301
26	X-RAY DIFFRACTION	16	F	0 - 100
27	X-RAY DIFFRACTION	17	F	101 - 127
28	X-RAY DIFFRACTION	17	F	183 - 254
29	X-RAY DIFFRACTION	18	F	128 - 182
30	X-RAY DIFFRACTION	18	F	301

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi