PDB-2b5a: C.BclI, Control Element of the BclI Restriction-Modification System

ID or keywords:

Entry

Database: PDB / ID: 2b5a

Title

C.BclI, Control Element of the BclI Restriction-Modification System

Components

C.BclI

Keywords

GENE REGULATION / HELIX-TURN-HELIX motif

Function / homology

lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Orthogonal Bundle / Mainly Alpha / ACETIC ACID

Function and homology information

Biological species

Bacillus caldolyticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.543 Å

Authors

Sawaya, M.R. / Zhu, Z. / Mersha, F. / Chan, S.H. / Dabur, R. / Xu, S.Y. / Balendiran, G.K.

Citation

Journal: Structure / Year: 2005
Title: Crystal Structure of the Restriction-Modification System Control Element C.BclI and Mapping of Its Binding Site.
Authors: Sawaya, M.R. / Zhu, Z. / Mersha, F. / Chan, S.H. / Dabur, R. / Xu, S.Y. / Balendiran, G.K.

History

Deposition	Sep 28, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 3, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Feb 14, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Remark 999

SEQUENCE THERE WAS NO SUITABLE SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2b5a.cif.gz	77.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2b5a.ent.gz	58.5 KB	Display	PDB format
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Others	Other downloads

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Validation report

Summary document	2b5a_validation.pdf.gz	445.3 KB	Display	wwPDB validaton report
Full document	2b5a_full_validation.pdf.gz	446.2 KB	Display
Data in XML	2b5a_validation.xml.gz	14.7 KB	Display
Data in CIF	2b5a_validation.cif.gz	21.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b5/2b5a ftp://data.pdbj.org/pub/pdb/validation_reports/b5/2b5a	HTTPS FTP

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Related structure data

Similar structure data	3ev6-1 4esn-d 5j1x-4 1kmz-d 2lla-d 6z92-1 2lt5-d 7d3d-1 6jfw-2 4b9f-2 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: C.BclI

B: C.BclI

C: C.BclI

D: C.BclI

hetero molecules

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

1

A: C.BclI

B: C.BclI

hetero molecules

defined by author&software
17.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: C.BclI

D: C.BclI

hetero molecules

defined by author&software
17.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.205, 65.016, 73.296
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

The biological assembly is a homodimer. Molecules A and B compose one biological assembly. Molecules C and D compose a second copy of the biological assembly.

#1: Protein	C.BclI Mass: 8931.332 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus caldolyticus (bacteria) / Gene: bclIC / Plasmid: LITMUS28 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2683
#2: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.19 Å³/Da / Density % sol: 43.3 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% (w/v) Polyethylene glyco 400, 25 mM ammonium sulfate, 50 mM citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL7-1	1	1.08
SYNCHROTRON	SSRL	BL1-5	2	1.0061, 1.0088, 0.9076

Detector

Type	ID	Detector	Date	Details
MARRESEARCH	1	IMAGE PLATE	Mar 27, 2002	58 cm long, Pt-coated, fused silica, vertical focusmirror, Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator
ADSC QUANTUM 4	2	CCD	May 24, 2002

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si (111)	SINGLE WAVELENGTH	M	x-ray	1
2		MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.08	1
2	1.0061	1
3	1.0088	1
4	0.9076	1

Reflection

ID	Number	R_merge(I) obs	Χ²	D res high (Å)	D res low (Å)	% possible obs
1	14246	0.042	1.069	1.6	200	69.5
2	14044	0.039	1.047	1.6	200	68.5
3	18212	0.046	1.124	1.6	200	88.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared
3.45	200	92.2	1	0.033	1.042
2.74	3.45	99.9	1	0.035	1.059
2.39	2.74	100	1	0.042	1.084
2.17	2.39	83.5	1	0.069	1.052
2.02	2.17	97.3	1	0.059	1.081
1.9	2.02	72.3	1	0.084	1.124
1.8	1.9	56.7	1	0.083	1.068
1.72	1.8	45.5	1	0.098	1.056
1.66	1.72	32.6	1	0.124	1.087
1.6	1.66	10.2	1	0.177	1.204
3.45	200	91.6	2	0.031	1.113
2.74	3.45	99.9	2	0.032	1.008
2.39	2.74	100	2	0.038	1.011
2.17	2.39	81.5	2	0.064	1.025
2.02	2.17	96.6	2	0.055	1.065
1.9	2.02	71.6	2	0.078	1.041
1.8	1.9	55.1	2	0.08	1.07
1.72	1.8	44.8	2	0.099	1.1
1.66	1.72	30.4	2	0.117	1.168
1.6	1.66	8.5	2	0.175	1.448
3.45	200	84.8	3	0.033	1.102
2.74	3.45	99.4	3	0.033	1.062
2.39	2.74	99.5	3	0.038	1.085
2.17	2.39	70.7	3	0.074	1.093
2.02	2.17	99.8	3	0.052	1.176
1.9	2.02	88.5	3	0.095	1.125
1.8	1.9	87.9	3	0.081	1.185
1.72	1.8	99.3	3	0.092	1.274
1.66	1.72	88	3	0.095	1.062
1.6	1.66	69.6	3	0.103	0.998

Reflection

Resolution: 1.54→99 Å / Num. all: 44934 / Num. obs: 44934 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / B_iso Wilson estimate: 28.3 Å² / R_merge(I) obs: 0.051 / Χ²: 1.59 / Net I/σ(I): 38

Reflection shell

Resolution: 1.54→1.56 Å / % possible obs: 68.4 % / R_merge(I) obs: 0.457 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 1526 / Num. unique all: 1526 / Χ²: 1.382 / % possible all: 68.4

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2 Å / D res low: 19.28 Å / FOM : 0.146 / FOM acentric: 0.142 / FOM centric: 0.17 / Reflection: 10001 / Reflection acentric: 8483 / Reflection centric: 1518

Phasing MAD set

Highest resolution: 2 Å

ID	R cullis acentric	R cullis centric	Lowest resolution (Å)	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	0.98	0.96	20	3.6	5	0.24	0.25	8175	1396
2	0.99	0.98	19.28	2.1	3.2	0.24	0.24	8465	1516
3	1.13	1	19.28	0	0	0	0	8483	1518

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	9.27-19.28	1.05	0.79	4.2	5.9	1.12	0.78	58	41
1	6.1-9.27	0.82	0.81	3.3	4.4	1.22	0.83	196	87
1	4.55-6.1	0.91	0.9	3.6	5.5	0.82	0.51	418	134
1	3.62-4.55	0.98	0.99	5.3	6.4	0.39	0.3	636	153
1	3.01-3.62	0.97	0.96	3	4.8	0.4	0.25	975	192
1	2.58-3.01	0.99	0.97	2.5	3.7	0.29	0.18	1573	267
1	2.25-2.58	1	1	3.1	4	0.13	0.09	1888	269
1	2-2.25	1	1	4.6	6.5	0.04	0.03	2431	253
2	9.27-19.28	0.91	0.96	3	3.9	1.03	0.75	58	53
2	6.1-9.27	0.86	0.9	2.5	3.6	1.01	0.67	196	100
2	4.55-6.1	0.92	0.94	2.1	3.5	0.86	0.51	418	145
2	3.62-4.55	0.98	1	2.6	3	0.47	0.38	676	175
2	3.01-3.62	0.99	0.98	1.8	2.7	0.38	0.24	1021	210
2	2.58-3.01	0.99	0.98	1.6	2.4	0.24	0.14	1573	276
2	2.25-2.58	1	1	1.7	2.9	0.11	0.06	1990	288
2	2-2.25	1	1	2.6	4.4	0.03	0.02	2533	269
3	9.27-19.28	2.41	1	0	0	0	0	58	53
3	6.1-9.27	1.89	1	0	0	0	0	196	100
3	4.55-6.1	1.37	1	0	0	0	0	418	145
3	3.62-4.55	0.93	1	0	0	0	0	682	175
3	3.01-3.62	0.93	1	0	0	0	0	1024	210
3	2.58-3.01	0.92	1	0	0	0	0	1573	276
3	2.25-2.58	1.05	1	0	0	0	0	1994	288
3	2-2.25	1	1	0	0	0	0	2538	271

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Hg	51.458	-0.848	-0.308	-0.195	0.029
2	Hg	63.984	-0.31	-0.827	-0.333	0.029
3	Hg	59.949	-0.848	-0.308	-0.196	0.02
4	Hg	72.973	-0.31	-0.83	-0.334	0.018
5	Hg	81.181	-0.849	-0.307	-0.197	0
6	Hg	86.413	-0.31	-0.831	-0.334	0

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
9.27-19.28	0.477	0.555	0.392	111	58	53
6.1-9.27	0.526	0.591	0.399	296	196	100
4.55-6.1	0.426	0.455	0.344	563	418	145
3.62-4.55	0.25	0.263	0.2	857	682	175
3.01-3.62	0.224	0.225	0.219	1234	1024	210
2.58-3.01	0.167	0.168	0.162	1849	1573	276
2.25-2.58	0.066	0.067	0.06	2282	1994	288
2-2.25	0.023	0.024	0.019	2809	2538	271

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 10001

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.7-100	55.9	0.769	504
4.5-5.7	55.4	0.764	503
3.92-4.5	58.2	0.654	505
3.45-3.92	69.6	0.301	502
3.22-3.45	72.3	0.345	501
3.03-3.22	70.6	0.482	502
2.88-3.03	76	0.203	501
2.76-2.88	80.2	0.455	501
2.65-2.76	85	0.33	506
2.56-2.65	90.2	0.385	507
2.48-2.56	89.9	0.104	503
2.41-2.48	85	0.33	511
2.35-2.41	83.8	0.18	507
2.29-2.35	89.1	0.187	512
2.2-2.29	94.5	0.03	504
2.15-2.2	87.8	0.026	512
2.11-2.15	83.8	0.025	515
2.07-2.11	89.3	0.021	518
2-2.07	88.4	0.249	887

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
Blu-Ice		data collection

Refinement

Method to determine structure:

MAD / Resolution: 1.543→19.741 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.959 / WR_factor R_free: 0.207 / WR_factor R_work: 0.168 / SU B: 2.677 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.079 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2005	2259	5.033 %	random
R_work	0.1652	-	-	-
all	0.167	44881	-	-
obs	0.167	44881	99.453 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.264 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.008 Å²	0 Å²	0 Å²
2-	-	-0.001 Å²	0 Å²
3-	-	-	-0.006 Å²

Refinement step

Cycle: LAST / Resolution: 1.543→19.741 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2461	0	8	229	2698

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	2500
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2416
X-RAY DIFFRACTION	r_angle_refined_deg	1.409	1.974	3332
X-RAY DIFFRACTION	r_angle_other_deg	1.441	3	5616
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.986	5	302
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	21.239	23.333	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.008	15	530
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.859	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	377
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2699
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	501
X-RAY DIFFRACTION	r_nbd_refined	0.24	0.2	583
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	2467
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1263
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	1457
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	142
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.317	0.2	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.268	0.2	72
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.139	0.2	26
X-RAY DIFFRACTION	r_symmetry_hbond_other	0.002	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.802	2	1566
X-RAY DIFFRACTION	r_mcbond_other	0.721	2	630
X-RAY DIFFRACTION	r_mcangle_it	3.414	3	2439
X-RAY DIFFRACTION	r_mcangle_other	2.022	3	2085
X-RAY DIFFRACTION	r_scbond_it	3.876	2	1015
X-RAY DIFFRACTION	r_scbond_other	1.323	2	1992
X-RAY DIFFRACTION	r_scangle_it	6.081	3	892
X-RAY DIFFRACTION	r_scangle_other	2.814	3	3531

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.543-1.583	0.3	161	0.21	2926	3285	93.973
1.583-1.626	0.254	168	0.185	3021	3189	100
1.626-1.673	0.237	165	0.187	2940	3105	100
1.673-1.724	0.22	150	0.175	2862	3012	100
1.724-1.78	0.212	159	0.173	2766	2926	99.966
1.78-1.842	0.208	136	0.164	2702	2839	99.965
1.842-1.911	0.214	141	0.161	2604	2745	100
1.911-1.988	0.194	138	0.161	2490	2628	100
1.988-2.075	0.171	126	0.158	2428	2554	100
2.075-2.175	0.168	111	0.152	2336	2447	100
2.175-2.291	0.174	106	0.148	2221	2327	100
2.291-2.428	0.156	87	0.144	2113	2200	100
2.428-2.593	0.186	100	0.155	1977	2077	100
2.593-2.797	0.19	104	0.157	1841	1945	100
2.797-3.058	0.227	91	0.167	1715	1806	100
3.058-3.409	0.2	81	0.162	1555	1637	99.939
3.409-3.917	0.188	98	0.153	1374	1472	100
3.917-4.75	0.174	50	0.161	1202	1260	99.365
4.75-6.531	0.227	52	0.215	970	1025	99.707
6.531-19.741	0.286	35	0.213	579	649	94.607

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	1.3267	0.5117	-0.7016	0.8334	-0.5792	2.5876	-0.0037	0.027	0.061	-0.0359	-0.012	-0.0164	-0.1156	0.196	0.0157	-0.0429	-0.0371	0.0071	-0.0498	-0.0058	-0.0535	20.7867	19.6463	1.1151
2	1.427	0.779	-0.4613	1.3415	-0.0939	1.3259	0.0409	-0.0819	-0.0002	0.0524	-0.0138	0.0069	0.0125	0.1112	-0.0271	-0.0456	0.0088	-0.0018	-0.0437	-0.0059	-0.0424	11.8343	11.0252	15.9207
3	1.4968	0.7045	-0.9097	1.8692	-0.1871	1.4245	0.037	0.1404	0.0398	-0.1277	-0.0737	0.0091	0.0088	0.0056	0.0367	-0.0415	0.0021	-0.0133	-0.0433	0.0238	-0.0566	20.9048	20.5389	38.2982
4	1.9478	0.9544	-0.2721	1.2284	-0.3536	0.8319	0.0599	-0.0639	0.0074	0.0713	-0.0859	0.0394	-0.0249	-0.0134	0.026	-0.0408	-0.0208	0.0049	-0.0517	-0.005	-0.0362	11.348	11.0627	52.1324

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 76	1 - 76
2	2	B	B	1 - 75	1 - 75
3	3	C	C	1 - 76	1 - 76
4	4	D	D	1 - 75	1 - 75

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