PDB-3kjk: Crystal structure of NMB1025, a member of YjgF protein family, fr...

ID or keywords:

Entry

Database: PDB / ID: 3kjk

Title

Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (monoclinic crystal form)

Components

NMB1025 protein

Keywords

UNKNOWN FUNCTION / NMB1025 / YjgF protein family / Neisseria meningitidis / OPPF / Structural Genomics / Oxford Protein Production Facility

Function / homology

Function and homology information

RutC family, YoaB-like / RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Neisseria meningitidis serogroup B (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

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

Citation

Journal: To be Published
Title: Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis
Authors: Ren, J. / Sainsbury, S. / Owens, R.J.

History

Deposition	Nov 3, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Sep 6, 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_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3	Nov 22, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3kjk.cif.gz	287.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3kjk.ent.gz	235.5 KB	Display	PDB format
PDBx/mmJSON format	3kjk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kj/3kjk ftp://data.pdbj.org/pub/pdb/validation_reports/kj/3kjk	HTTPS FTP

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Related structure data

Related structure data	3kjjSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3kjj-3 3kjj-6 3kjj-5 3kjj-2 3kjj-4 3kjj-1 6do4-1 3k1u-d 3i7t-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) 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: OPTIC7114

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1)

Deposited unit

A: NMB1025 protein

B: NMB1025 protein

C: NMB1025 protein

D: NMB1025 protein

E: NMB1025 protein

F: NMB1025 protein

G: NMB1025 protein

H: NMB1025 protein

I: NMB1025 protein

J: NMB1025 protein

K: NMB1025 protein

L: NMB1025 protein

173 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NMB1025 protein

B: NMB1025 protein

C: NMB1025 protein

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

2

D: NMB1025 protein

E: NMB1025 protein

F: NMB1025 protein

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

3

G: NMB1025 protein

H: NMB1025 protein

I: NMB1025 protein

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

4

J: NMB1025 protein

K: NMB1025 protein

L: NMB1025 protein

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

Unit cell

Length a, b, c (Å)	117.032, 78.275, 181.871
Angle α, β, γ (deg.)	90.00, 103.62, 90.00
Int Tables number	5
Space group name H-M	C121

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
9	1	I
10	1	J
11	1	K
12	1	L

#1: Protein	NMB1025 protein Mass: 14426.478 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Strain: MC58 / Gene: NMB1025 / Plasmid: OPPF1359 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9JZJ4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.34 Å³/Da / Density % sol: 47.4 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: di-Potassium Hydrogen Phosphate 1.2 M, Sodium di-Hydrogen Phosphate 0.6 M, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 24, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.29→30 Å / Num. obs: 69756 / % possible obs: 96.4 % / Observed criterion σ(I): -1.5 / Redundancy: 6.3 % / R_merge(I) obs: 0.165 / Net I/σ(I): 15
Reflection shell	Resolution: 2.29→2.37 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.996 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6500 / % possible all: 90.6

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Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KJJ

3kjj

Resolution: 2.29→30 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.871 / SU B: 16.451 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25907	3518	5.1 %	RANDOM
R_work	0.22062	-	-	-
obs	0.2226	66128	96.55 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 15.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.29 Å²	0 Å²	1.89 Å²
2-	-	-2.45 Å²	0 Å²
3-	-	-	2.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.29→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10810	0	0	575	11385

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	11026
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.966	1.937	14978
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.521	5	1382
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.621	22.955	528
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.898	15	1752
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.352	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	1634
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	8528
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	2.359	4	6898
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	4.814	8	10982
X-RAY DIFFRACTION	r_scbond_it	6.604	8	4128
X-RAY DIFFRACTION	r_scangle_it	11.115	16	3996
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 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	464	medium positional	0.14	20
B	464	medium positional	0.13	20
C	464	medium positional	0.11	20
D	464	medium positional	0.11	20
E	464	medium positional	0.13	20
F	464	medium positional	0.11	20
G	464	medium positional	0.15	20
H	464	medium positional	0.26	20
I	464	medium positional	0.16	20
J	464	medium positional	0.18	20
K	464	medium positional	0.15	20
L	464	medium positional	0.14	20
A	436	loose positional	0.37	30
B	436	loose positional	0.39	30
C	436	loose positional	0.4	30
D	436	loose positional	0.41	30
E	436	loose positional	0.5	30
F	436	loose positional	0.49	30
G	436	loose positional	0.78	30
H	436	loose positional	0.67	30
I	436	loose positional	0.4	30
J	436	loose positional	0.66	30
K	436	loose positional	0.32	30
L	436	loose positional	0.49	30
A	464	medium thermal	0.54	2
B	464	medium thermal	0.51	2
C	464	medium thermal	0.55	2
D	464	medium thermal	0.62	2
E	464	medium thermal	0.59	2
F	464	medium thermal	0.61	2
G	464	medium thermal	0.5	2
H	464	medium thermal	0.47	2
I	464	medium thermal	0.49	2
J	464	medium thermal	0.42	2
K	464	medium thermal	0.48	2
L	464	medium thermal	0.42	2
A	436	loose thermal	0.64	10
B	436	loose thermal	0.57	10
C	436	loose thermal	0.56	10
D	436	loose thermal	0.66	10
E	436	loose thermal	0.59	10
F	436	loose thermal	0.61	10
G	436	loose thermal	0.49	10
H	436	loose thermal	0.51	10
I	436	loose thermal	0.51	10
J	436	loose thermal	0.48	10
K	436	loose thermal	0.5	10
L	436	loose thermal	0.54	10

LS refinement shell

Resolution: 2.29→2.349 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	244	-
R_work	0.301	4647	-
obs	-	-	92.02 %

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	0.6532	0.2013	-0.3477	0.7779	-0.0143	0.4277	-0.0158	-0.1096	0.0294	0.1186	-0.0223	0.0461	-0.0344	0.0284	0.0381	0.1715	-0.0082	-0.097	0.1912	-0.0008	0.1753	7.653	-27.401	25.071
2	0.2686	-0.1201	0.3587	0.8367	-0.4246	0.5847	-0.0534	0.0019	0.0264	0.1079	0.0748	0.0258	-0.0526	-0.0331	-0.0214	0.2222	-0.0035	-0.07	0.2461	0.0036	0.1324	2.05	-42.793	37.904
3	0.64	-0.1412	0.0909	0.473	0.0931	0.5061	-0.0371	0.0179	-0.0056	0.0439	0.0087	-0.0495	-0.003	-0.1116	0.0284	0.1638	0.0059	-0.0717	0.1774	-0.0094	0.1611	10.19	-47.112	19.178
4	0.3661	-0.3521	0.1387	0.3443	-0.1043	0.3559	0.078	0.0386	-0.0521	-0.0529	-0.025	0.0333	-0.0106	-0.0025	-0.053	0.1791	0.0028	-0.1058	0.181	-0.0081	0.1577	-29.752	-49.981	6.611
5	0.1534	0.1126	0.2348	0.6786	-0.085	0.4925	0.0352	-0.0266	-0.0137	0.067	0.0402	0.0765	0.0128	-0.013	-0.0754	0.1575	-0.0133	-0.065	0.1891	-0.0075	0.1588	-35.769	-38.47	22.867
6	0.9687	-0.2025	-0.0092	0.056	-0.017	0.0653	-0.0088	0.0776	-0.0172	0.0253	-0.0419	0.0213	-0.0634	0.0867	0.0507	0.1623	-0.0054	-0.0832	0.19	0.0207	0.1972	-28.889	-29.303	5.427
7	0.9378	-0.2207	-0.387	0.2123	0.0664	1.7077	-0.0174	-0.0376	-0.1463	0.1145	0.0136	-0.0221	-0.0009	-0.0126	0.0039	0.3376	0.0492	-0.0843	0.2332	0.0053	0.1546	27.293	-6.922	66.568
8	0.3931	-0.0706	0.0942	1.4266	0.0145	0.3317	-0.0225	-0.0764	-0.1427	-0.126	0.0178	0.057	0.0402	-0.2466	0.0047	0.4229	-0.0098	-0.0241	0.2378	0.0256	0.2089	7.926	-12.079	60.953
9	0.2183	-0.455	-0.3408	1.2942	0.2627	1.1163	-0.0218	0.0091	0.0167	0.0861	0.0847	-0.0034	-0.0334	-0.1244	-0.063	0.371	0.0103	-0.051	0.2045	0.0004	0.1396	20.235	-1.465	47.858
10	0.5937	0.4084	-0.6637	0.3146	-0.486	1.8948	0.0497	-0.1579	0.0318	0.1418	-0.0547	0.0176	-0.1699	0.3039	0.005	0.4785	0.071	-0.0867	0.2975	-0.0558	0.1538	14.658	31.226	78.336
11	0.64	0.2228	-0.2561	0.0992	0.0249	0.9308	0.056	-0.0457	0.0894	0.0591	0.0083	0.0244	-0.0114	-0.0086	-0.0643	0.3768	0.0546	-0.0518	0.2132	0.0239	0.1636	1.124	32.067	62.55
12	1.1006	-0.3582	0.346	0.5839	-0.41	1.4885	-0.0317	-0.1848	0.0811	0.1917	0.0709	0.0125	0.1964	-0.1605	-0.0392	0.4184	0.0719	-0.0331	0.2681	0.0117	0.15	-3.974	22.348	80.302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 116
2	X-RAY DIFFRACTION	1	A	121 - 603
3	X-RAY DIFFRACTION	2	B	1 - 116
4	X-RAY DIFFRACTION	2	B	121 - 606
5	X-RAY DIFFRACTION	3	C	1 - 116
6	X-RAY DIFFRACTION	3	C	121 - 604
7	X-RAY DIFFRACTION	4	D	1 - 117
8	X-RAY DIFFRACTION	4	D	121 - 595
9	X-RAY DIFFRACTION	5	E	1 - 116
10	X-RAY DIFFRACTION	5	E	121 - 599
11	X-RAY DIFFRACTION	6	F	1 - 116
12	X-RAY DIFFRACTION	6	F	121 - 578
13	X-RAY DIFFRACTION	7	G	1 - 116
14	X-RAY DIFFRACTION	7	G	121 - 590
15	X-RAY DIFFRACTION	8	H	1 - 116
16	X-RAY DIFFRACTION	8	H	121 - 576
17	X-RAY DIFFRACTION	9	I	1 - 116
18	X-RAY DIFFRACTION	9	I	121 - 596
19	X-RAY DIFFRACTION	10	J	1 - 116
20	X-RAY DIFFRACTION	10	J	121 - 588
21	X-RAY DIFFRACTION	11	K	1 - 116
22	X-RAY DIFFRACTION	11	K	121 - 598
23	X-RAY DIFFRACTION	12	L	1 - 117
24	X-RAY DIFFRACTION	12	L	121 - 561

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