PDB-2i45: Crystal structure of protein NMB1881 from Neisseria meningitidis

ID or keywords:

Entry

Database: PDB / ID: 2i45

Title

Crystal structure of protein NMB1881 from Neisseria meningitidis

Components

Hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Neisseria meningitidis Cupin domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Cupin_2 domain-containing protein

Function and homology information

Biological species

Neisseria meningitidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Chang, C. / Hatzos, C. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of protein NMB1881 from Neisseria meningitidis
Authors: Chang, C. / Hatzos, C. / Bargassa, M. / Joachimiak, A.

History

Deposition	Aug 21, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2i45.cif.gz	201.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2i45.ent.gz	173.5 KB	Display	PDB format
PDBx/mmJSON format	2i45.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2i45_validation.pdf.gz	516.2 KB	Display	wwPDB validaton report
Full document	2i45_full_validation.pdf.gz	562.7 KB	Display
Data in XML	2i45_validation.xml.gz	42.6 KB	Display
Data in CIF	2i45_validation.cif.gz	59.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i4/2i45 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/2i45	HTTPS FTP

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Related structure data

Similar structure data	6cay-2 4tky-2 3q36-1 4kvs-d 4g29-d 2w2r-d 1r4v-d 2rci-d 6cay-1 3ra5-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetDB: APC83736

Similar structure data

Other databases

TargetDB: APC83736

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein

B: Hypothetical protein

C: Hypothetical protein

D: Hypothetical protein

E: Hypothetical protein

F: Hypothetical protein

G: Hypothetical protein

H: Hypothetical protein

I: Hypothetical protein

J: Hypothetical protein

122 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hypothetical protein

B: Hypothetical protein

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

2

C: Hypothetical protein

D: Hypothetical protein

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

3

E: Hypothetical protein

F: Hypothetical protein

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

4

G: Hypothetical protein

H: Hypothetical protein

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

5

I: Hypothetical protein

J: Hypothetical protein

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

Unit cell

Length a, b, c (Å)	94.932, 94.932, 155.704
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Hypothetical protein Mass: 12198.138 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: NMB1881 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q9JXU4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.87 Å³/Da / Density % sol: 57.22 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: K/Na Tartrate, CHES, Lithium sulfate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2006
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97935 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. all: 47392 / Num. obs: 46681 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / R_merge(I) obs: 0.095 / Net I/σ(I): 21.9
Reflection shell	Resolution: 2.5→2.52 Å / Redundancy: 8.3 % / R_merge(I) obs: 0.455 / Mean I/σ(I) obs: 1.4 / Num. unique all: 968 / % possible all: 82.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-2000		data reduction
HKL-2000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→50 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.911 / SU B: 22.402 / SU ML: 0.24 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26793	2366	5.1 %	RANDOM
R_work	0.19897	-	-	-
all	0.20245	44271	-	-
obs	0.20245	44271	98.49 %	-

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: 52.679 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.17 Å²	0 Å²	0 Å²
2-	-	-3.17 Å²	0 Å²
3-	-	-	6.34 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7682	0	0	243	7925

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.021	7862
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.26	1.932	10622
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.317	5	959
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.486	24.016	376
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.246	15	1323
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.953	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.157	0.2	1149
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5962
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.275	0.2	3677
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.333	0.2	5055
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.253	0.2	433
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	0.275	0.2	76
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.162	0.2	8
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	1.325	1.5	4956
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.669	2	7673
X-RAY DIFFRACTION	r_scbond_it	2.782	3	3353
X-RAY DIFFRACTION	r_scangle_it	3.973	4.5	2949
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.568 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	169	-
R_work	0.277	2817	-
obs	-	-	85.9 %

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	3.9699	-1.1888	-0.5967	10.6987	-1.8806	3.2141	0.2198	0.1808	0.1671	-0.1199	-0.0648	1.1805	0.3662	-0.1773	-0.1549	0.1385	-0.0248	-0.0446	-0.1823	-0.0165	-0.2167	16.415	1.673	32.677
2	3.59	-2.7027	-0.1588	8.297	8.3038	12.3039	0.4465	0.4401	0.234	0.0618	-0.5279	-0.1397	-0.4446	-0.3054	0.0814	0.152	0.0729	-0.0357	-0.063	0.0243	-0.2637	27.132	-7.914	30.937
3	7.7519	-2.919	-0.2952	5.807	0.6597	0.6973	0.1833	0.6672	0.0238	-0.1799	-0.1877	-0.4552	0.1611	0.2432	0.0044	0.149	0.0193	0.0253	-0.0289	0.0544	-0.2586	25.842	15.859	30.661
4	6.0178	-1.8119	4.7138	3.3435	-4.5804	7.2638	-0.0259	-0.0643	-0.1562	0.075	-0.0106	0.4402	0.2796	0.1507	0.0365	0.0824	0.0562	0.0232	-0.0958	-0.043	-0.0219	14.775	25.367	33.746
5	4.3598	-1.3602	-0.4751	5.8627	-0.9303	2.8882	-0.0754	0.0489	0.2625	0.1805	0.0473	0.5511	-0.3431	-0.1453	0.0282	0.113	-0.0355	0.0522	-0.1494	-0.0172	0.0297	17.047	51.533	47.035
6	0.888	0.7694	1.077	5.2315	4.0683	7.9107	0.0119	-0.203	0.0695	-0.1153	-0.0093	0.105	-0.2405	0.0543	-0.0027	0.0073	-0.0436	0.0338	-0.1248	0.0721	-0.0401	23.171	38.719	45.981
7	3.8989	-0.687	0.9638	8.4325	-0.2385	3.3887	-0.1301	0.1402	-0.2498	0.4798	-0.24	-0.7718	-0.5786	0.2207	0.3701	0.2262	-0.1431	-0.068	-0.2103	0.0614	-0.1066	30.853	60.595	43.967
8	1.4164	1.2735	1.3749	10.4523	-5.4016	6.0683	0.4168	-0.1057	-0.4056	0.3872	-0.2346	-0.0825	0.4795	0.2051	-0.1822	0.5315	-0.055	-0.0961	-0.1441	-0.0313	-0.109	24.804	73.738	45.519
9	3.2381	-1.7322	-0.733	6.4206	-1.2088	2.2392	0.0564	0.2557	-0.085	-0.1792	0.0392	0.6569	-0.0662	-0.2721	-0.0956	0.0203	-0.0129	-0.0561	-0.1395	-0.0363	0.0152	-28.337	-8.938	32.08
10	0.4516	-0.4807	-1.1563	3.4487	4.8343	8.9754	0.0781	-0.1693	0.18	0.0829	-0.11	-0.3292	-0.7035	-0.1165	0.032	0.0968	0.0578	-0.0637	-0.1176	0.0257	-0.1136	-17.236	-18.279	32.557
11	4.2114	-3.129	-0.7901	8.0378	0.3436	2.3054	0.0681	0.1873	-0.0176	-0.128	-0.0929	-0.5106	0.0933	0.0615	0.0248	0.0577	0.0097	-0.0096	-0.142	0.0277	-0.1225	-18.83	5.056	29.879
12	7.808	-3.3566	4.8109	6.4291	-3.9852	8.2281	0.4655	0.5428	-0.0108	0.2586	-0.2348	0.708	0.1502	0.2137	-0.2307	0.0406	0.0331	-0.0163	-0.0744	0.0261	-0.1942	-29.554	14.641	30.295
13	5.5857	-0.043	-0.2433	6.6676	-1.3655	3.1742	0.1773	0.2366	0.5047	0.0737	-0.0486	0.5872	0.1909	-0.108	-0.1287	0.0561	-0.0575	-0.0359	-0.1439	0.0154	-0.1404	-29.569	41.269	45.055
14	3.9969	-0.2549	-3.4451	6.0176	1.9401	5.3554	-0.0777	0.1174	-0.2433	-0.0843	0.1019	-0.2591	-0.2403	-0.0662	-0.0242	0.1187	-0.0272	-0.0608	-0.0728	0.0533	-0.1954	-23.634	28.302	43.972
15	3.1407	-1.1349	-0.0341	6.8446	-0.2254	1.7234	0.0573	0.1189	-0.2038	-0.036	-0.0471	-0.3051	0.0236	0.0868	-0.0102	0.0572	-0.0439	0.0387	-0.0898	-0.0111	-0.18	-15.431	50.573	44.549
16	1.4569	0.3287	2.5689	6.4959	-3.9463	7.7194	-0.0643	-0.2137	-0.0306	0.1284	-0.0446	0.4152	0.1671	0.1516	0.1088	0.0751	0.0212	0.0329	-0.1081	-0.0559	-0.0583	-21.564	63.387	46.913
17	7.838	-2.5193	0.3587	4.345	0.0812	2.4591	-0.145	0.5158	0.3764	-0.0543	0.0107	-0.4391	0.0063	0.2503	0.1343	0.0004	0.0177	-0.0011	-0.0346	0.0276	-0.0879	-2.684	58.338	17.707
18	5.2622	-2.7081	5.6014	6.7781	-3.5861	8.2839	0.1922	0.3268	-0.2151	-0.2415	-0.1144	-0.169	0.6344	-0.0394	-0.0778	0.0432	0.0374	0.0504	0.0488	-0.0255	-0.3631	-17.222	60.792	19.096
19	7.8825	-1.2743	-0.3311	3.8784	-1.3347	2.6739	0.0055	0.6291	-0.3341	-0.1616	0.0559	0.2126	0.1037	0.0723	-0.0614	0.0463	0.0447	-0.0198	-0.0493	-0.084	-0.1607	-3.334	41.333	19.428
20	7.7302	-1.1288	-2.6946	7.6619	6.0399	8.866	0.1782	0.994	0.2153	-0.429	-0.2488	-0.1156	-0.6504	-0.0361	0.0706	0.0222	0.0917	-0.0463	0.0433	0.028	-0.0784	11.37	38.875	18.849

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	4 - 37	4 - 37
2	X-RAY DIFFRACTION	1	A	A	48 - 56	48 - 56
3	X-RAY DIFFRACTION	1	A	A	74 - 82	74 - 82
4	X-RAY DIFFRACTION	1	A	A	93 - 101	93 - 101
5	X-RAY DIFFRACTION	2	A	A	38 - 45	38 - 45
6	X-RAY DIFFRACTION	2	A	A	57 - 73	57 - 73
7	X-RAY DIFFRACTION	2	A	A	83 - 92	83 - 92
8	X-RAY DIFFRACTION	3	B	B	4 - 37	4 - 37
9	X-RAY DIFFRACTION	3	B	B	47 - 56	47 - 56
10	X-RAY DIFFRACTION	3	B	B	74 - 82	74 - 82
11	X-RAY DIFFRACTION	3	B	B	93 - 101	93 - 101
12	X-RAY DIFFRACTION	4	B	B	38 - 44	38 - 44
13	X-RAY DIFFRACTION	4	B	B	57 - 73	57 - 73
14	X-RAY DIFFRACTION	4	B	B	83 - 92	83 - 92
15	X-RAY DIFFRACTION	5	C	C	4 - 37	4 - 37
16	X-RAY DIFFRACTION	5	C	C	47 - 56	47 - 56
17	X-RAY DIFFRACTION	5	C	C	74 - 82	74 - 82
18	X-RAY DIFFRACTION	5	C	C	93 - 101	93 - 101
19	X-RAY DIFFRACTION	6	C	C	38 - 46	38 - 46
20	X-RAY DIFFRACTION	6	C	C	57 - 73	57 - 73
21	X-RAY DIFFRACTION	6	C	C	83 - 92	83 - 92
22	X-RAY DIFFRACTION	7	D	D	4 - 37	4 - 37
23	X-RAY DIFFRACTION	7	D	D	47 - 56	47 - 56
24	X-RAY DIFFRACTION	7	D	D	74 - 82	74 - 82
25	X-RAY DIFFRACTION	7	D	D	93 - 101	93 - 101
26	X-RAY DIFFRACTION	8	D	D	38 - 46	38 - 46
27	X-RAY DIFFRACTION	8	D	D	57 - 73	57 - 73
28	X-RAY DIFFRACTION	8	D	D	83 - 92	83 - 92
29	X-RAY DIFFRACTION	9	E	E	4 - 37	4 - 37
30	X-RAY DIFFRACTION	9	E	E	47 - 56	47 - 56
31	X-RAY DIFFRACTION	9	E	E	74 - 82	74 - 82
32	X-RAY DIFFRACTION	9	E	E	93 - 101	93 - 101
33	X-RAY DIFFRACTION	10	E	E	38 - 45	38 - 45
34	X-RAY DIFFRACTION	10	E	E	57 - 73	57 - 73
35	X-RAY DIFFRACTION	10	E	E	83 - 92	83 - 92
36	X-RAY DIFFRACTION	11	F	F	4 - 37	4 - 37
37	X-RAY DIFFRACTION	11	F	F	47 - 56	47 - 56
38	X-RAY DIFFRACTION	11	F	F	74 - 82	74 - 82
39	X-RAY DIFFRACTION	11	F	F	93 - 101	93 - 101
40	X-RAY DIFFRACTION	12	F	F	38 - 46	38 - 46
41	X-RAY DIFFRACTION	12	F	F	57 - 73	57 - 73
42	X-RAY DIFFRACTION	12	F	F	83 - 92	83 - 92
43	X-RAY DIFFRACTION	13	G	G	4 - 37	4 - 37
44	X-RAY DIFFRACTION	13	G	G	47 - 56	47 - 56
45	X-RAY DIFFRACTION	13	G	G	74 - 82	74 - 82
46	X-RAY DIFFRACTION	13	G	G	93 - 101	93 - 101
47	X-RAY DIFFRACTION	14	G	G	38 - 46	38 - 46
48	X-RAY DIFFRACTION	14	G	G	57 - 73	57 - 73
49	X-RAY DIFFRACTION	14	G	G	83 - 92	83 - 92
50	X-RAY DIFFRACTION	15	H	H	4 - 37	4 - 37
51	X-RAY DIFFRACTION	15	H	H	47 - 56	47 - 56
52	X-RAY DIFFRACTION	15	H	H	74 - 82	74 - 82
53	X-RAY DIFFRACTION	15	H	H	93 - 101	93 - 101
54	X-RAY DIFFRACTION	16	H	H	38 - 46	38 - 46
55	X-RAY DIFFRACTION	16	H	H	57 - 73	57 - 73
56	X-RAY DIFFRACTION	16	H	H	83 - 92	83 - 92
57	X-RAY DIFFRACTION	17	I	I	4 - 37	4 - 37
58	X-RAY DIFFRACTION	17	I	I	48 - 56	48 - 56
59	X-RAY DIFFRACTION	17	I	I	74 - 82	74 - 82
60	X-RAY DIFFRACTION	17	I	I	93 - 101	93 - 101
61	X-RAY DIFFRACTION	18	I	I	38 - 45	38 - 45
62	X-RAY DIFFRACTION	18	I	I	57 - 73	57 - 73
63	X-RAY DIFFRACTION	18	I	I	83 - 92	83 - 92
64	X-RAY DIFFRACTION	19	J	J	4 - 37	4 - 37
65	X-RAY DIFFRACTION	19	J	J	49 - 56	49 - 56
66	X-RAY DIFFRACTION	19	J	J	74 - 82	74 - 82
67	X-RAY DIFFRACTION	19	J	J	93 - 101	93 - 101
68	X-RAY DIFFRACTION	20	J	J	38 - 45	38 - 45
69	X-RAY DIFFRACTION	20	J	J	57 - 73	57 - 73
70	X-RAY DIFFRACTION	20	J	J	83 - 92	83 - 92

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