PDB-1vl5: CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (BH2331) FROM B...

ID or keywords:

Entry

Database: PDB / ID: 1vl5

Title

CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (BH2331) FROM BACILLUS HALODURANS C-125 AT 1.95 A RESOLUTION

Components

unknown conserved protein BH2331

Keywords

TRANSFERASE / PUTATIVE METHYLTRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI

Function / homology

Function and homology information

S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function

Biological species

Bacillus halodurans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.95 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of hypothetical protein (BH2331) from Bacillus halodurans at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jul 9, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 17, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Jan 25, 2023	Group: Database references / Derived calculations / Category: database_2 / 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 1.4	Nov 13, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Remark 999

1. THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHHM] FOLLOWED BY ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1vl5.cif.gz	204.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vl/1vl5 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/1vl5	HTTPS FTP

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Related structure data

Similar structure data	1j6r-2 2og8-1 2h34-2 2h34-1 6tfw-2 4dap-d 1oey-1 3va4-d 1xxl-2 3rk6-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetDB: 354314 TargetDB: 356107 TargetDB: 356108 TargetDB: 356109 TargetDB: 356110 TargetDB: 356111 TargetDB: 356112 TargetDB: 356489 TargetDB: 356490 TargetDB: 356491 TargetDB: 356492 TargetDB: 356493 TargetDB: 356494 TargetDB: 356495 TargetDB: 356496 TargetDB: 356497

Similar structure data

Other databases

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: unknown conserved protein BH2331

B: unknown conserved protein BH2331

C: unknown conserved protein BH2331

D: unknown conserved protein BH2331

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

1

A: unknown conserved protein BH2331

defined by author
30.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: unknown conserved protein BH2331

defined by author
30.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: unknown conserved protein BH2331

defined by author
30.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: unknown conserved protein BH2331

defined by author
30.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.006, 87.475, 105.236
Angle α, β, γ (deg.)	90.00, 100.57, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 6

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	SER	SER	A	A	28 - 147	23 - 142
2	1	1	GLY	GLY	SER	SER	B	B	28 - 147	23 - 142
3	1	1	GLY	GLY	SER	SER	C	C	28 - 147	23 - 142
4	1	1	GLY	GLY	SER	SER	D	D	28 - 147	23 - 142
5	2	1	ALA	ALA	ILE	ILE	A	A	172 - 200	167 - 195
6	2	1	ALA	ALA	ILE	ILE	B	B	172 - 200	167 - 195
7	2	1	ALA	ALA	ILE	ILE	C	C	172 - 200	167 - 195
8	2	1	ALA	ALA	ILE	ILE	D	D	172 - 200	167 - 195
9	3	1	ARG	ARG	THR	THR	A	A	241 - 258	236 - 253
10	3	1	ARG	ARG	THR	THR	B	B	241 - 258	236 - 253
11	3	1	ARG	ARG	THR	THR	C	C	241 - 258	236 - 253
12	3	1	ARG	ARG	THR	THR	D	D	241 - 258	236 - 253
1	1	2	ALA	ALA	ARG	ARG	A	A	148 - 171	143 - 166
2	1	2	ALA	ALA	ARG	ARG	B	B	148 - 171	143 - 166
3	1	2	ALA	ALA	ARG	ARG	C	C	148 - 171	143 - 166
4	1	2	ALA	ALA	ARG	ARG	D	D	148 - 171	143 - 166
5	2	2	PHE	PHE	GLY	GLY	A	A	201 - 240	196 - 235
6	2	2	PHE	PHE	GLY	GLY	B	B	201 - 240	196 - 235
7	2	2	PHE	PHE	GLY	GLY	C	C	201 - 240	196 - 235
8	2	2	PHE	PHE	GLY	GLY	D	D	201 - 240	196 - 235

NCS ensembles :

ID
1
2

#1: Protein	unknown conserved protein BH2331 Mass: 30243.199 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2331 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KAF6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.64 Å³/Da / Density % sol: 53.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop Details: 12% PEG MME 2000, 0.04M Acetic Acid, 0.06M Citrate_Na3 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 0.979494,0.885567,0.979494

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2004 / Details: flat mirror

Radiation

Monochromator: single crystal Si(311) bent monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979494	1
2	0.885567	1

Reflection

Resolution: 1.85→49.83 Å / Num. obs: 90667 / % possible obs: 93.2 % / Redundancy: 3.6 % / B_iso Wilson estimate: 31.44 Å² / R_sym value: 0.083 / Net I/σ(I): 11.8

Reflection shell

Resolution: 1.85→1.9 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 4475 / R_sym value: 0.523 / % possible all: 62.9

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	4.2)	data scaling
SOLVE		phasing
RESOLVE		model building
REFMAC	5.2.0001	refinement
CCP4	(SCALA)	data scaling
RESOLVE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.95→49.83 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.938 / SU B: 7.233 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOMS AND RESIDUES THAT COULD NOT BE RESOLVED WERE NOT BUILT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20882	4191	5 %	RANDOM
R_work	0.17726	-	-	-
obs	0.1789	78937	100 %	-

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: 27.757 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.36 Å²	0 Å²	-0.29 Å²
2-	-	2.16 Å²	0 Å²
3-	-	-	-0.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→49.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7186	0	0	634	7820

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	7379
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6538
X-RAY DIFFRACTION	r_angle_refined_deg	1.513	1.934	9968
X-RAY DIFFRACTION	r_angle_other_deg	0.808	3	15152
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.61	5	904
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.617	24.05	363
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.929	15	1234
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.704	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1062
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8302
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1599
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	1491
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	6378
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	4319
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	572
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.072	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.229	0.2	92
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.194	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	2.459	3	4859
X-RAY DIFFRACTION	r_mcbond_other	0.646	3	1846
X-RAY DIFFRACTION	r_mcangle_it	2.963	5	7232
X-RAY DIFFRACTION	r_scbond_it	5.361	8	3169
X-RAY DIFFRACTION	r_scangle_it	6.872	11	2736
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	3641

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	2199	loose positional	0.41	5
1	2	B	2199	loose positional	0.43	5
1	3	C	2199	loose positional	0.9	5
1	4	D	2199	loose positional	0.44	5
1	1	A	2199	loose thermal	2.24	10
1	2	B	2199	loose thermal	2.42	10
1	3	C	2199	loose thermal	3.77	10
1	4	D	2199	loose thermal	2.06	10
2	1	A	981	loose positional	0.22	5
2	2	B	981	loose positional	0.28	5
2	3	C	981	loose positional	0.3	5
2	4	D	981	loose positional	0.29	5
2	1	A	981	loose thermal	1.98	10
2	2	B	981	loose thermal	1.94	10
2	3	C	981	loose thermal	2.14	10
2	4	D	981	loose thermal	2.4	10

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	280	4.56 %
R_work	0.227	5859	-
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	0.092	0.0909	0.1326	0.9933	-0.0253	0.3359	-0.0051	0.0132	0.0098	-0.0978	-0.0141	-0.0044	0.1465	0.0727	0.0191	-0.1104	0.0004	-0.0018	-0.1362	0.0027	-0.1654	42.708	11.785	80.155
2	0.5756	0.0015	-0.0327	0.5627	-0.1493	1.3497	-0.0202	0.065	-0.0067	-0.1497	0.0105	0.0093	0.1811	0.1621	0.0097	-0.1104	0.0124	-0.0001	-0.1125	0.0275	-0.1439	72.542	38.291	53.476
3	1.0506	0.2808	0.4957	0.5183	0.3062	1.2934	0.0272	-0.1982	-0.0045	0.1979	-0.0322	0.0756	0.062	-0.1751	0.0051	-0.0947	0.0072	-0.0059	-0.1333	0.0013	-0.1452	40.707	30.563	104.65
4	2.7403	0.6186	-0.0873	0.8093	-0.0081	0.9396	-0.0025	0.0894	0.7332	-0.0478	0.0655	0.0131	-0.308	-0.0311	-0.063	-0.0542	-0.0073	0.0058	-0.1331	0.0304	0.1198	33.697	20.788	31.061
5	4.0604	-0.3116	0.0494	0.9967	-0.6927	1.8392	-0.0757	0.3014	-0.2396	-0.0886	-0.0189	-0.092	0.2334	0.2188	0.0946	-0.1639	-0.0143	0.016	-0.1167	0.0048	-0.144	63.457	26.023	79.205
6	3.8745	0.2217	0.6275	1.3345	-0.3317	1.6836	-0.0261	0.2338	-0.1409	-0.1858	0.0067	0.116	0.1187	-0.0847	0.0194	-0.1514	-0.0123	0.005	-0.1596	0.0163	-0.1035	51.533	37.494	67.58
7	4.0849	1.6956	0.5474	1.6195	-0.089	1.501	0.0249	-0.4168	0.409	0.1751	-0.0914	0.2678	-0.0913	-0.4405	0.0665	-0.1681	0.0461	-0.0086	-0.0326	-0.021	-0.0872	19.395	36.336	92.943
8	3.1226	-0.196	-0.3442	1.766	0.2957	1.2002	-0.0538	0.2357	0.2929	-0.1215	0.0696	0.1541	-0.1848	-0.0915	-0.0158	-0.1434	-0.0163	-0.0378	-0.1109	0.0311	-0.1024	13.237	7.184	25.296

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	28 - 147	23 - 142
2	1	A	A	172 - 200	167 - 195
3	1	A	A	241 - 258	236 - 253
4	2	B	B	28 - 147	23 - 142
5	2	B	B	172 - 200	167 - 195
6	2	B	B	241 - 258	236 - 253
7	3	C	C	28 - 147	23 - 142
8	3	C	C	172 - 200	167 - 195
9	3	C	C	241 - 258	236 - 253
10	4	D	D	28 - 147	23 - 142
11	4	D	D	172 - 200	167 - 195
12	4	D	D	241 - 258	236 - 253
13	5	A	A	148 - 171	143 - 166
14	5	A	A	201 - 240	196 - 235
15	6	B	B	148 - 171	143 - 166
16	6	B	B	201 - 240	196 - 235
17	7	C	C	148 - 171	143 - 166
18	7	C	C	201 - 240	196 - 235
19	8	D	D	148 - 171	143 - 166
20	8	D	D	201 - 240	196 - 235

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