PDB-3lwi: Crystal structure of Cren7-dsDNA complex

ID or keywords:

Entry

Database: PDB / ID: 3lwi

Title

Crystal structure of Cren7-dsDNA complex

Components

Chromatin protein Cren7
DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

Keywords

DNA BINDING PROTEIN/DNA / Protein-DNA complex / beta-sheet / DNA-binding / Methylation / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

double-stranded DNA binding / cytoplasm
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Zhang, Z.F. / Gong, Y. / Guo, L. / Jiang, T. / Huang, L.

Citation

Journal: Mol.Microbiol. / Year: 2010
Title: Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA
Authors: Zhang, Z.F. / Gong, Y. / Guo, L. / Jiang, T. / Huang, L.

History

Deposition	Feb 23, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 26, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Mar 5, 2014	Group: Database references
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3lwi.cif.gz	57.3 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	3lwi.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3lwi_validation.pdf.gz	442.8 KB	Display	wwPDB validaton report
Full document	3lwi_full_validation.pdf.gz	443.5 KB	Display
Data in XML	3lwi_validation.xml.gz	8.7 KB	Display
Data in CIF	3lwi_validation.cif.gz	11.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lw/3lwi ftp://data.pdbj.org/pub/pdb/validation_reports/lw/3lwi	HTTPS FTP

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Related structure data

Related structure data	3lwhC 2jtmS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5wvz-2 5k17-2 5wvy-1 5wvw-1 5wvy-2 5wvz-1 4r56-2 5wvw-2 3lwh-d 4r56-1 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Chromatin protein Cren7

B: Chromatin protein Cren7

C: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

D: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

E: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

F: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

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

1

A: Chromatin protein Cren7

C: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

D: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

defined by author&software
11.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Chromatin protein Cren7

E: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

F: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')

defined by author&software
11.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.443, 77.232, 105.020
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	1 - 8
2	1	1	2	B	1 - 8
1	2	1	2	A	10 - 60
2	2	1	2	B	10 - 60
1	1	2	1	C	101 - 108
2	1	2	1	E	101 - 108
1	1	3	1	D	109 - 116
2	1	3	1	F	109 - 116

NCS ensembles :

ID
1
2
3

#1: Protein	Chromatin protein Cren7 Mass: 6677.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: creN7, SSO6901 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) plysS / References: UniProt: Q97ZE3
#2: DNA chain	DNA (5'-D(GPCPGPAPTPCPGPC)-3') Mass: 2427.605 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.4 Å³/Da / Density % sol: 63.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.8 Details: 30% PEG1500, pH 6.8, VAPOR DIFFUSION, temperature 293.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97947 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. obs: 15270 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / R_merge(I) obs: 0.065 / R_sym value: 0.052 / Net I/σ(I): 39.6
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 8.3 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 4.8 / R_sym value: 0.32 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JTM

2jtm

Resolution: 2.3→30 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.945 / SU B: 9.626 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.234 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23351	721	5 %	RANDOM
R_work	0.20335	-	-	-
all	0.20489	13592	-	-
obs	0.20489	13592	99.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 44.581 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.98 Å²	0 Å²	0 Å²
2-	-	0.58 Å²	0 Å²
3-	-	-	-2.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	914	644	0	115	1673

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1660
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.373	2.479	2368
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.704	5	114
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	21.356	23.333	30
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.075	15	182
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.028	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	254
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1020
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.17	0.2	530
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	981
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	124
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	0.171	0.2	30
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.099	0.2	6
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	0.728	1.5	596
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.848	2	942
X-RAY DIFFRACTION	r_scbond_it	0.965	3	1438
X-RAY DIFFRACTION	r_scangle_it	1.411	4.5	1426
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 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	228	tight positional	0.04	0.05
2	C	161	tight positional	0.01	0.05
3	D	161	tight positional	0.01	0.05
1	A	220	medium positional	0.29	0.5
1	A	228	tight thermal	0.02	0.5
2	C	161	tight thermal	0.04	0.5
3	D	161	tight thermal	0.04	0.5
1	A	220	medium thermal	0.13	2

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.33	48	-
R_work	0.281	980	-
obs	-	-	100 %

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	13.9928	-2.7664	2.9999	5.2775	-0.5727	6.5166	0.1597	0.0026	0.8069	-0.3271	-0.3009	0.7005	-0.6675	-1.1171	0.1411	-0.0451	0.1081	-0.0391	0.005	-0.1187	-0.0584	16.977	21.904	-32.863
2	12.7916	3.486	3.1164	8.8829	2.2673	6.9901	-0.1965	0.2195	0.2828	-0.1561	-0.0419	0.9109	-0.0123	-0.5411	0.2384	-0.1546	0.0794	-0.0426	-0.0599	-0.0389	-0.2111	18.082	17.813	-34.669
3	5.1234	2.7851	0.2213	12.9299	2.0231	6.368	-0.1588	0.3276	-0.7183	-0.0368	0.076	0.6429	1.0417	-0.7248	0.0829	-0.0332	-0.1038	0.1081	-0.0301	-0.0532	-0.0601	16.82	16.885	-6.607
4	12.0008	-6.384	-2.9113	13.7184	4.7422	6.6347	-0.0615	0.2632	-0.9353	-0.1856	-0.1375	0.3859	0.528	-0.0977	0.1991	-0.0489	-0.0887	0.0433	-0.1481	-0.0222	-0.2172	20.875	18.027	-8.407
5	5.4929	1.2241	0.3201	2.8758	1.2474	4.012	-0.0229	0.1981	-0.1292	-0.2654	-0.0111	-0.1093	0.0618	0.1458	0.0339	-0.188	-0.0081	-0.0179	-0.1624	-0.0165	-0.2562	28.46	12.71	-36.695
6	2.9935	-1.6242	-1.419	6.0164	0.5178	3.4096	-0.0358	0.2174	0.0872	-0.203	0.0323	-0.0945	-0.1251	0.094	0.0035	-0.16	0.0123	0.0049	-0.1696	-0.009	-0.2593	25.99	28.389	-10.44

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 12
2	X-RAY DIFFRACTION	1	A	15 - 29
3	X-RAY DIFFRACTION	2	A	36 - 43
4	X-RAY DIFFRACTION	2	A	47 - 53
5	X-RAY DIFFRACTION	3	B	8 - 12
6	X-RAY DIFFRACTION	3	B	15 - 29
7	X-RAY DIFFRACTION	4	B	36 - 43
8	X-RAY DIFFRACTION	4	B	47 - 53
9	X-RAY DIFFRACTION	5	C	101 - 108
10	X-RAY DIFFRACTION	5	D	109 - 116
11	X-RAY DIFFRACTION	6	E	101 - 108
12	X-RAY DIFFRACTION	6	F	109 - 116

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