PDB-2p5v: Crystal Structure of Transcriptional Regulator NMB0573 from Neiss...

ID or keywords:

Entry

Database: PDB / ID: 2p5v

Title

Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis

Components

Transcriptional regulator, LRP/AsnC family

Keywords

TRANSCRIPTION / NMB0573 / Transcriptional regulator / Lrp/AsnC-family / Structural Genomics / Structural and functional analysis of N. meninigitidis transcriptional regulators / Oxford Protein Production Facility / OPPF

Function / homology

Function and homology information

response to amino acid / sequence-specific DNA binding / regulation of DNA-templated transcription / metal ion binding / cytosol
Similarity search - Function

Biological species

Neisseria meningitidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.99 Å

Authors

Ren, J. / Sainsbury, S. / Owens, R.J. / Oxford Protein Production Facility (OPPF)

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: The Structure and Transcriptional Analysis of a Global Regulator from Neisseria meningitidis.
Authors: Ren, J. / Sainsbury, S. / Combs, S.E. / Capper, R.G. / Jordan, P.W. / Berrow, N.S. / Stammers, D.K. / Saunders, N.J. / Owens, R.J.

History

Deposition	Mar 16, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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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PDBx/mmCIF format	2p5v.cif.gz	274 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2p5v_validation.pdf.gz	499.4 KB	Display	wwPDB validaton report
Full document	2p5v_full_validation.pdf.gz	515.1 KB	Display
Data in XML	2p5v_validation.xml.gz	63.3 KB	Display
Data in CIF	2p5v_validation.cif.gz	82 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p5/2p5v ftp://data.pdbj.org/pub/pdb/validation_reports/p5/2p5v	HTTPS FTP

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Related structure data

Related structure data	2p6sC 2p6tC C: citing same article (ref.)
Similar structure data	2p6t-d 2p6s-d 2qz8-1 2w25-1 2ivm-1 2w24-1 3i4p-1 2cg4-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: OPTIC224

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator, LRP/AsnC family

B: Transcriptional regulator, LRP/AsnC family

C: Transcriptional regulator, LRP/AsnC family

D: Transcriptional regulator, LRP/AsnC family

E: Transcriptional regulator, LRP/AsnC family

F: Transcriptional regulator, LRP/AsnC family

G: Transcriptional regulator, LRP/AsnC family

H: Transcriptional regulator, LRP/AsnC family

hetero molecules

148 kDa, 8 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)	65.070, 148.480, 77.720
Angle α, β, γ (deg.)	90.00, 106.41, 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
7	1	G
8	1	H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 5 - 158 / Label seq-ID: 7 - 160

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
7	G	G
8	H	H

#1: Protein	Transcriptional regulator, LRP/AsnC family Mass: 18288.701 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0573 / Plasmid: OPPF2146 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9K0L9
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 95 mM HEPES-Na, 190 mM Calcium Chloride, 26.6% PEG 400, 5% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: BM14 / Wavelength: 0.9795, 0.9078

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2005 / Details: mirrors

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9795	1
2	0.9078	1

Reflection

Resolution: 2→30 Å / Num. obs: 74733 / % possible obs: 77.7 % / Observed criterion σ(I): -1.5 / Redundancy: 7.4 % / B_iso Wilson estimate: 26 Å² / R_merge(I) obs: 0.082 / Net I/σ(I): 20.2

Reflection shell

Resolution: 2→2.07 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.424 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2860 / % possible all: 29.9

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Processing

Software

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

Refinement

Method to determine structure:

MAD / Resolution: 1.99→29.59 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.93 / SU B: 9.882 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23785	3804	5.1 %	RANDOM
R_work	0.17624	-	-	-
obs	0.17933	70865	77.14 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 39.879 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.85 Å²	0 Å²	4 Å²
2-	-	-0.58 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→29.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9844	0	66	760	10670

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	10053
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6828
X-RAY DIFFRACTION	r_angle_refined_deg	1.1	1.974	13601
X-RAY DIFFRACTION	r_angle_other_deg	0.821	3	16693
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.566	5	1236
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.527	23.996	453
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.076	15	1807
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.081	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	1617
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10961
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1987
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	2033
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	7215
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	4743
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	5580
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	598
X-RAY DIFFRACTION	r_metal_ion_refined	0.097	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.201	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.235	0.2	79
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.113	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	3.667	4	6456
X-RAY DIFFRACTION	r_mcbond_other	1.27	4	2479
X-RAY DIFFRACTION	r_mcangle_it	4.711	6	10035
X-RAY DIFFRACTION	r_scbond_it	6.354	6	4024
X-RAY DIFFRACTION	r_scangle_it	8.789	10	3566

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	913	medium positional	0.45	0.5
2	B	913	medium positional	0.23	0.5
3	C	913	medium positional	0.24	0.5
4	D	913	medium positional	0.62	0.5
5	E	913	medium positional	0.28	0.5
6	F	913	medium positional	0.22	0.5
7	G	913	medium positional	0.33	0.5
8	H	913	medium positional	0.38	0.5
1	A	1144	loose positional	1.08	5
2	B	1144	loose positional	0.88	5
3	C	1144	loose positional	0.91	5
4	D	1144	loose positional	1.12	5
5	E	1144	loose positional	0.98	5
6	F	1144	loose positional	0.89	5
7	G	1144	loose positional	0.86	5
8	H	1144	loose positional	1.04	5
1	A	913	medium thermal	3.08	20
2	B	913	medium thermal	3	20
3	C	913	medium thermal	3.28	20
4	D	913	medium thermal	3.37	20
5	E	913	medium thermal	3.1	20
6	F	913	medium thermal	3.42	20
7	G	913	medium thermal	2.78	20
8	H	913	medium thermal	3.4	20
1	A	1144	loose thermal	4.3	30
2	B	1144	loose thermal	4.67	30
3	C	1144	loose thermal	4.58	30
4	D	1144	loose thermal	4.36	30
5	E	1144	loose thermal	4.71	30
6	F	1144	loose thermal	4.86	30
7	G	1144	loose thermal	3.94	30
8	H	1144	loose thermal	4.42	30

LS refinement shell

Resolution: 1.989→2.04 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	81	-
R_work	0.264	1657	-
obs	-	-	24.36 %

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	1.6299	-0.5892	-0.7241	5.3096	2.8531	2.9875	0.047	-0.1577	0.1384	0.3824	0.0241	0.1309	0.023	-0.0404	-0.0712	-0.1282	-0.0027	-0.0158	-0.0588	0.0129	-0.1136	5.666	18.538	88.062
2	1.3591	0.0619	-0.4133	2.0815	0.3662	1.4537	-0.0195	0.1813	0.0872	-0.1624	-0.0197	0.0892	0.0182	-0.0936	0.0392	-0.2032	-0.0057	-0.0608	-0.0465	0.0102	-0.1428	15.975	9.136	60.801
3	4.5458	2.8603	-1.1782	3.6137	-0.6576	2.2546	0.0326	0.1147	-0.0026	0.0823	0.039	0.1642	0.1042	-0.2995	-0.0716	-0.1577	0.0056	-0.0421	-0.0357	0.0092	-0.1847	-2.672	1.792	78.101
4	1.5831	0.856	-0.0327	1.685	0.2733	1.1198	0.0312	-0.1357	0.0495	0.1363	-0.0374	-0.1267	0.0756	0.1761	0.0062	-0.1361	0.009	-0.0366	-0.0457	0.0057	-0.1851	26.193	10.928	72.82
5	1.0622	2.2377	-1.6194	7.9949	-2.7758	2.5921	-0.1279	-0.0737	-0.096	0.0594	-0.0105	0.2872	0.2227	0.0205	0.1384	-0.0166	-0.0395	-0.047	-0.0222	-0.01	-0.0212	20.073	-33.225	50.321
6	1.7475	0.3502	-0.7808	2.1811	-0.4172	2.0002	-0.0614	0.2029	0.0782	-0.116	0.085	0.113	-0.0436	-0.0492	-0.0236	-0.159	-0.0471	-0.0954	-0.041	-0.0228	-0.1877	30.211	-5.788	40.84
7	2.814	-0.1391	-1.4333	3.1037	1.9523	5.3853	-0.2494	0.4711	-0.8217	-0.6523	0.0153	-0.4569	0.462	0.2002	0.2341	0.1325	-0.0548	0.0055	0.1049	-0.0895	0.1993	30.635	-29.706	31.281
8	1.5581	0.4168	-0.3551	1.7775	0.4951	2.2779	-0.0814	-0.1262	-0.0894	0.1328	0.0455	-0.0066	0.0944	0.0814	0.0359	-0.1247	-0.0093	-0.0439	-0.1068	0.008	-0.1668	32.99	-10.825	55.607
9	2.8273	-1.8622	-2.7269	4.0308	2.0263	5.4618	-0.1483	-0.0541	-0.247	0.0717	0.0406	-0.0573	0.6492	0.3812	0.1077	-0.0116	-0.0193	-0.029	0.0522	-0.0088	-0.1483	70.079	-0.554	23.468
10	1.9968	-0.0432	-0.7628	1.9336	-0.0966	1.2309	0.0155	0.152	0.1588	-0.1252	0.0894	0.0644	-0.0618	-0.1686	-0.1049	-0.1009	-0.0437	-0.035	-0.0172	0.01	-0.2116	48.149	16.119	36.905
11	4.732	2.2298	-2.3294	3.5172	-1.0749	1.9778	0.087	0.2229	0.4361	-0.2013	0.0856	0.0002	-0.2816	0.0345	-0.1726	-0.0575	-0.0307	-0.0108	0.0666	-0.0235	-0.0984	70.821	20.308	23.898
12	0.806	0.2046	-0.2508	1.032	-0.0509	1.4656	-0.0016	0.0254	-0.0227	-0.027	0.0744	-0.1078	0.0752	-0.0103	-0.0728	-0.1776	-0.0083	-0.0382	-0.0383	-0.0358	-0.1424	54.896	4.125	44.683
13	10.6565	3.6639	-3.2906	2.7396	-2.4804	3.6348	0.1546	-0.5277	0.5943	-0.0318	-0.3031	-0.3595	-0.3795	0.6389	0.1485	0.1816	-0.0588	-0.0403	0.07	-0.0348	0.293	56.713	50.975	61.63
14	2.7394	-0.1039	-0.3807	1.8493	-0.0974	1.6924	0.0726	0.0905	0.2368	-0.099	-0.0037	0.1549	-0.0698	-0.1162	-0.0689	-0.1353	0.0149	-0.0293	-0.0983	0.031	-0.1006	33.957	31.061	56.8
15	4.3013	-5.0474	-1.4485	10.9726	1.7461	0.4883	-0.2258	-0.3753	0.3039	0.832	0.4369	-0.1983	-0.1625	0.1225	-0.2112	0.1049	-0.0004	-0.0257	0.0448	-0.0703	0.0504	36.351	53.833	69.577
16	2.7186	-0.4496	-0.6988	2.3914	0.1714	1.3065	0.0317	-0.1772	0.1179	0.0438	0.0379	-0.2799	0.0239	0.1981	-0.0696	-0.1623	-0.0283	-0.1013	-0.0136	-0.0431	-0.1495	47.992	26.051	61.923

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	3 - 60	5 - 62
2	X-RAY DIFFRACTION	2	A	A	61 - 158	63 - 160
3	X-RAY DIFFRACTION	3	B	B	3 - 60	5 - 62
4	X-RAY DIFFRACTION	4	B	B	61 - 158	63 - 160
5	X-RAY DIFFRACTION	5	C	C	5 - 60	7 - 62
6	X-RAY DIFFRACTION	6	C	C	61 - 158	63 - 160
7	X-RAY DIFFRACTION	7	D	D	3 - 60	5 - 62
8	X-RAY DIFFRACTION	8	D	D	61 - 158	63 - 160
9	X-RAY DIFFRACTION	9	E	E	3 - 60	5 - 62
10	X-RAY DIFFRACTION	10	E	E	61 - 158	63 - 160
11	X-RAY DIFFRACTION	11	F	F	5 - 60	7 - 62
12	X-RAY DIFFRACTION	12	F	F	61 - 158	63 - 160
13	X-RAY DIFFRACTION	13	G	G	1 - 60	3 - 62
14	X-RAY DIFFRACTION	14	G	G	61 - 158	63 - 160
15	X-RAY DIFFRACTION	15	H	H	5 - 60	7 - 62
16	X-RAY DIFFRACTION	16	H	H	61 - 158	63 - 160

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi