PDB-3dky: Crystal Structure of the replication initiator protein encoded on...

ID or keywords:

Entry

Database: PDB / ID: 3dky

Title

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), tetragonal form, to 3.6 Ang resolution

Components

Replication protein repB

Keywords

REPLICATION / Replication initiation / Plasmid replication / Nuclease / Hexamer / Flexible nuclease domains / DNA replication / Plasmid / REPLICATION INITIATOR

Function / homology

Function and homology information

DNA topoisomerase activity / extrachromosomal circular DNA / DNA replication / DNA binding / identical protein binding
Similarity search - Function

Biological species

Streptococcus agalactiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.6 Å

Authors

Boer, D.R. / Ruiz-Maso, J.A. / Blanco, A.G. / Vives-Llacer, M. / Uson, I. / Gomis-Ruth, F.X. / Espinosa, M. / Del Solar, G. / Coll, M.

Citation

Journal: Embo J. / Year: 2009
Title: Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains
Authors: Boer, D.R. / Ruiz-Maso, J.A. / Lopez-Blanco, J.R. / Blanco, A.G. / Vives-Llacer, M. / Chacon, P. / Uson, I. / Gomis-Ruth, F.X. / Espinosa, M. / Llorca, O. / del Solar, G. / Coll, M.

History

Deposition	Jun 26, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 30, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3dky.cif.gz	487.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3dky.ent.gz	411.7 KB	Display	PDB format
PDBx/mmJSON format	3dky.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3dky_validation.pdf.gz	478.4 KB	Display	wwPDB validaton report
Full document	3dky_full_validation.pdf.gz	523.4 KB	Display
Data in XML	3dky_validation.xml.gz	46.1 KB	Display
Data in CIF	3dky_validation.cif.gz	61.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dk/3dky ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dky	HTTPS FTP

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Related structure data

Related structure data	3dkxSC 1ksx 1ksy 1l2m 1rz9 2gxa 2hw0 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	430 3r6s-d 4hax-d 6agq-d 1zxv-d 5ng6-4 1633 431 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

Deposited unit

A: Replication protein repB

B: Replication protein repB

C: Replication protein repB

D: Replication protein repB

E: Replication protein repB

F: Replication protein repB

hetero molecules

146 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	91.460, 91.460, 227.080
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A and resid 135:203	A	135 - 203
2	1	1	chain B and resid 135:203	B	135 - 203
3	1	1	chain C and resid 135:203	C	135 - 203
4	1	1	chain D and resid 135:203	D	135 - 203
5	1	1	chain E and resid 135:203	E	135 - 203
6	1	1	chain F and resid 135:203	F	135 - 203
1	1	2	chain A and (resid 4:129 or resid 301)	A	0
2	1	2	chain D and (resid 4:129 or resid 301)	D	0
3	1	2	chain F and (resid 4:129 or resid 301)	F	0
4	1	2	chain E and (resid 4:129 or resid 301)	E	0
5	1	2	chain B and (resid 4:129 or resid 301)	B	0
6	1	2	chain C and (resid 4:129 or resid 301)	C	0
1	1	3	chain B and resid 130:134	B	130 - 134
2	1	3	chain D and resid 130:134	D	130 - 134
3	1	3	chain F and resid 130:134	F	130 - 134
1	1	4	chain A and resid 130:134	A	130 - 134
2	1	4	chain C and resid 130:134	C	130 - 134
3	1	4	chain E and resid 130:134	E	130 - 134

NCS ensembles :

ID
1
2
3
4

#1: Protein	Replication protein repB Mass: 24287.105 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: repB / Plasmid details: repB (plasmid pMV158) / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P13921
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

#1: Protein

Replication protein repB

Mass: 24287.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus agalactiae (bacteria) / Gene: repB / Plasmid details: repB (plasmid pMV158) / Plasmid: pGEM-T / Production host:

Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P13921

#2: Chemical

ChemComp-MN / MANGANESE (II) ION

Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.26 Å³/Da / Density % sol: 62.26 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 10% PEG 4000, 0.2mM MgCl2, 50mM CHES, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.005 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 23, 2004
Radiation	Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.005 Å / Relative weight: 1
Reflection	Resolution: 3.6→25 Å / Num. obs: 21350 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / R_merge(I) obs: 0.075 / Net I/σ(I): 10.95
Reflection shell	Resolution: 3.6→3.85 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.462 / Mean I/σ(I) obs: 3.01 / Num. measured all: 7763 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
ProDC	(ESRF)	data collection
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
AMoRE		phasing
MOLREP		phasing
PHENIX	1.4_4	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DKX

3dkx

Resolution: 3.6→19.571 Å / Occupancy max: 1 / Occupancy min: 1 / SU B: 64.622 / SU ML: -0 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2567	1098	5.14 %	RANDOM
R_work	0.2234	20252	-	-
obs	0.2251	21350	99.7 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 74.996 Å² / k_sol: 0.284 e/Å³

Displacement parameters

B_iso max: 317.99 Å² / B_iso mean: 158.604 Å² / B_iso min: 90.23 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.741 Å²	0 Å²	0 Å²
2-	-	0.741 Å²	-0 Å²
3-	-	-	-1.482 Å²

Refine analyze

Luzzati coordinate error obs: 0.827 Å

Refinement step

Cycle: LAST / Resolution: 3.6→19.571 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9459	0	4	0	9463

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	9644
X-RAY DIFFRACTION	f_angle_d	1.67	13025
X-RAY DIFFRACTION	f_chiral_restr	0.093	1492
X-RAY DIFFRACTION	f_plane_restr	0.005	1617
X-RAY DIFFRACTION	f_dihedral_angle_d	20.058	3528

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	560	X-RAY DIFFRACTION	POSITIONAL	0.09
1	2	B	560	X-RAY DIFFRACTION	POSITIONAL	0.09
1	3	C	560	X-RAY DIFFRACTION	POSITIONAL	0.098
1	4	D	560	X-RAY DIFFRACTION	POSITIONAL	0.086
1	5	E	560	X-RAY DIFFRACTION	POSITIONAL	0.089
1	6	F	560	X-RAY DIFFRACTION	POSITIONAL	0.078
2	1	A	936	X-RAY DIFFRACTION	POSITIONAL	0.089
2	2	D	936	X-RAY DIFFRACTION	POSITIONAL	0.089
2	3	F	937	X-RAY DIFFRACTION	POSITIONAL	0.093
2	4	E	863	X-RAY DIFFRACTION	POSITIONAL	0.086
2	5	B	1027	X-RAY DIFFRACTION	POSITIONAL	0.093
2	6	C	1027	X-RAY DIFFRACTION	POSITIONAL	0.091
3	1	B	45	X-RAY DIFFRACTION	POSITIONAL	0.1
3	2	D	45	X-RAY DIFFRACTION	POSITIONAL	0.1
3	3	F	45	X-RAY DIFFRACTION	POSITIONAL	0.105
4	1	A	45	X-RAY DIFFRACTION	POSITIONAL	0.093
4	2	C	45	X-RAY DIFFRACTION	POSITIONAL	0.093
4	3	E	45	X-RAY DIFFRACTION	POSITIONAL	0.078

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 (%)
3.6-3.7628	0.3282	144	0.3288	2513	X-RAY DIFFRACTION	100
3.7628-3.9596	0.3126	159	0.3014	2531	X-RAY DIFFRACTION	100
3.9596-4.2054	0.3298	143	0.269	2495	X-RAY DIFFRACTION	100
4.2054-4.5264	0.2735	123	0.236	2556	X-RAY DIFFRACTION	100
4.5264-4.9751	0.2272	137	0.2156	2545	X-RAY DIFFRACTION	100
4.9751-5.6796	0.215	129	0.2046	2551	X-RAY DIFFRACTION	100
5.6796-7.0985	0.2465	122	0.2046	2548	X-RAY DIFFRACTION	100
7.0985-19.5709	0.2038	141	0.174	2513	X-RAY DIFFRACTION	98

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	8.6612	0.1084	1.8805	10.5214	0.5327	2.7389	-0.2635	-0.0355	-0.2492	-0.7526	-0.6119	0.6264	0.1837	-1.4407	0.0037	0.4614	-0.0317	-0.0522	1.0959	-0.7006	0.9578	-9.7598	23.1084	-7.8916
2	8.6352	-1.2997	5.8045	8.7821	0.3205	3.8573	0.1073	-0.9102	-1.0641	-0.5721	-0.875	1.3998	0.8118	0.0499	-0.0081	0.6213	-0.2117	0.0593	0.8119	-0.4873	0.4156	3.9701	10.2132	-5.3808
3	6.7795	-2.0993	5.9783	9.277	3.0746	5.6821	0.0897	-0.5125	-0.1096	0.8054	-0.1938	-0.2187	0.3972	-0.029	0.0003	0.642	-0.1355	0.0157	0.4587	-0.1598	0.2691	18.8288	13.9836	6.1162
4	8.3792	-4.7415	3.6138	6.411	2.6828	8.9634	0.2569	-0.3313	0.2482	0.9231	-0.372	-0.5998	-0.8964	0.1075	0.0044	0.8798	-0.0097	-0.1535	0.4187	-0.3064	0.5464	20.212	30.7127	15.2396
5	7.7557	-0.8842	2.3	4.0206	4.2705	5.339	-0.2123	0.1464	0.8339	0.2631	0.0483	-0.2884	-0.5085	-0.9013	0.002	0.6884	-0.0248	0.0072	0.7345	-0.5478	1.0757	6.2596	43.7845	12.8172
6	7.0081	-1.4281	2.2919	7.342	3.9899	3.6608	0.1005	-0.175	0.6475	0.3035	-0.6191	0.915	0.22	-1.4105	0.002	0.5467	-0.0479	0.0666	1.1299	-0.683	1.1802	-8.6033	39.9471	1.3163
7	11.1205	-2.6999	3.8195	5.1743	1.3896	4.4648	-2.3025	1.6127	2.1223	-0.6118	0.2594	-0.3686	-2.6933	1.7968	-1.4704	-1.1584	0.3836	1.0325	0.2759	-0.2425	-0.5355	13.4233	19.1758	-39.0564
8	6.5908	1.2993	2.0718	2.1983	0.1869	4.5508	-0.3496	-0.7092	-0.3112	-0.1157	0.4761	-1.5347	0.8721	0.7553	0.3221	0.0766	0.113	0.3637	0.5515	0.0825	0.3341	36.0136	3.0952	-23.0698
9	3.4022	-3.8547	-1.2065	0.6963	2.2566	2.0866	0.3991	0.265	0.7111	-0.0901	0.2347	-0.2342	-0.2157	0.7996	0.0001	0.6511	-0.2843	0.3383	1.1546	-0.4599	1.065	48.5741	35.4937	-8.067
10	2.6779	-3.5832	-1.3516	4.2381	1.5709	2.761	0.2857	-0.0971	1.0661	-0.2208	0.8154	-2.2093	-0.665	1.0921	-0.0016	1.5412	-0.1225	0.3332	1.2003	-0.4103	2.2365	40.4253	60.7898	9.242
11	-1.6565	0.6955	0.7457	2.177	-3.5338	0.5989	-0.2802	0.8552	1.0691	-0.0301	-0.116	-0.1474	-0.9738	0.48	0.0007	2.3908	-0.3965	-0.3083	2.0593	-0.0899	2.4892	2.3499	63.4472	-18.5613
12	-0.6636	-0.7219	0.8421	-0.108	2.3025	1.0585	0.0334	0.1453	1.3262	0.1357	-0.1852	0.2931	-1.5698	0.3914	-0.0057	1.0789	-0.2204	0.2861	1.6625	-0.4608	1.3306	-18.3432	43.7841	-31.6714

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and resid 135:203	A	135 - 203
2	X-RAY DIFFRACTION	2	chain B and resid 135:203	B	135 - 203
3	X-RAY DIFFRACTION	3	chain C and resid 135:203	C	135 - 203
4	X-RAY DIFFRACTION	4	chain D and resid 135:203	D	135 - 203
5	X-RAY DIFFRACTION	5	chain E and resid 135:203	E	135 - 203
6	X-RAY DIFFRACTION	6	chain F and resid 135:203	F	135 - 203
7	X-RAY DIFFRACTION	7	chain A and (resid 4:134 or resid 301)	A	0
8	X-RAY DIFFRACTION	8	chain B and (resid 4:134 or resid 301)	B	0
9	X-RAY DIFFRACTION	9	chain C and (resid 4:134 or resid 301)	C	0
10	X-RAY DIFFRACTION	10	chain D and (resid 4:134 or resid 301)	D	0
11	X-RAY DIFFRACTION	11	chain E and (resid 4:134 or resid 301)	E	0
12	X-RAY DIFFRACTION	12	chain F and (resid 4:134 or resid 301)	F	0

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