PDB-3eey: CRYSTAL STRUCTURE OF PUTATIVE RRNA-METHYLASE FROM Clostridium the...

Basic information

• Entry: Database: PDB / ID: 3eey
• Title: CRYSTAL STRUCTURE OF PUTATIVE RRNA-METHYLASE FROM Clostridium thermocellum
• Components: Putative rRNA methylase
• Keywords: TRANSFERASE / RRNA METHYLATION / S-ADENOSYL-METHIONINE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / METHYLTRANSFERASE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS

Function / homology

Function:

methyltransferase activity / methylation

Domain/homology:

Putative rRNA methylase / Putative rRNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

S-ADENOSYLMETHIONINE / rRNA methylase

• Biological species: Clostridium thermocellum ATCC 27405 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
• Authors: Patskovsky, Y. / Ramagopal, U.A. / Toro, R. / Rutter, M. / Hu, S. / Bain, K. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
• Citation: Journal: To be Published; Title: Crystal Structure of Rrna-Methylase from Clostridium Thermocellum; Authors: Patskovsky, Y. / Ramagopal, U.A. / Toro, R. / Rutter, M. / Hu, S. / Bain, K. / Sauder, J.M. / Burley, S.K. / Almo, S.C.

History

Deposition	Sep 6, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Nov 14, 2018	Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3	Feb 10, 2021	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Assembly

Deposited unit

A: Putative rRNA methylase

B: Putative rRNA methylase

C: Putative rRNA methylase

D: Putative rRNA methylase

E: Putative rRNA methylase

F: Putative rRNA methylase

G: Putative rRNA methylase

H: Putative rRNA methylase

I: Putative rRNA methylase

J: Putative rRNA methylase

hetero molecules

Summary:

• 223 kDa, 10 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	222,814	28
Polymers	218,380	10
Non-polymers	4,435	18
Water	6,485	360

1

A: Putative rRNA methylase

C: Putative rRNA methylase

hetero molecules

Summary:

• defined by author&software
• 44.9 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,949	9
Polymers	43,676	2
Non-polymers	1,273	7
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	3120 Å2
ΔGint	-46 kcal/mol
Surface area	17200 Å2
Method	PISA

2

B: Putative rRNA methylase

D: Putative rRNA methylase

hetero molecules

Summary:

• defined by author&software
• 44.7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,661	6
Polymers	43,676	2
Non-polymers	985	4
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	2880 Å2
ΔGint	-30 kcal/mol
Surface area	17040 Å2
Method	PISA

3

E: Putative rRNA methylase

H: Putative rRNA methylase

hetero molecules

Summary:

• defined by author&software
• 44.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,565	5
Polymers	43,676	2
Non-polymers	889	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	2620 Å2
ΔGint	-11 kcal/mol
Surface area	16270 Å2
Method	PISA

4

F: Putative rRNA methylase

I: Putative rRNA methylase

hetero molecules

Summary:

• defined by author&software
• 44.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,565	5
Polymers	43,676	2
Non-polymers	889	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	2770 Å2
ΔGint	-9 kcal/mol
Surface area	16240 Å2
Method	PISA

5

G: Putative rRNA methylase

J: Putative rRNA methylase

hetero molecules

Summary:

• defined by author&software
• 44.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,074	3
Polymers	43,676	2
Non-polymers	398	1
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	2550 Å2
ΔGint	-11 kcal/mol
Surface area	16210 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	70.156, 126.913, 125.611
Angle α, β, γ (deg.)	90.00, 99.54, 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
9	1	I
10	1	J
1	2	A
2	2	B
3	2	C
4	2	D
5	2	E
6	2	F
7	2	G
8	2	H
9	2	I
10	2	J

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-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	THR	THR	TYR	TYR	A	A	2 - 138	4 - 140
2	1	THR	THR	TYR	TYR	B	B	2 - 138	4 - 140
3	1	THR	THR	TYR	TYR	C	C	2 - 138	4 - 140
4	1	THR	THR	TYR	TYR	D	D	2 - 138	4 - 140
5	1	THR	THR	TYR	TYR	E	E	2 - 138	4 - 140
6	1	THR	THR	TYR	TYR	F	F	2 - 138	4 - 140
7	1	THR	THR	TYR	TYR	G	G	2 - 138	4 - 140
8	1	THR	THR	TYR	TYR	H	H	2 - 138	4 - 140
9	1	THR	THR	TYR	TYR	I	I	2 - 138	4 - 140
10	1	THR	THR	TYR	TYR	J	J	2 - 138	4 - 140
1	2	GLU	GLU	GLY	GLY	A	A	147 - 189	149 - 191
2	2	GLU	GLU	GLU	GLU	B	B	147 - 188	149 - 190
3	2	GLU	GLU	GLY	GLY	C	C	147 - 189	149 - 191
4	2	GLU	GLU	GLY	GLY	D	D	147 - 189	149 - 191
5	2	GLU	GLU	GLY	GLY	E	E	147 - 189	149 - 191
6	2	GLU	GLU	GLY	GLY	F	F	147 - 189	149 - 191
7	2	GLU	GLU	GLY	GLY	G	G	147 - 189	149 - 191
8	2	GLU	GLU	GLY	GLY	H	H	147 - 189	149 - 191
9	2	GLU	GLU	ILE	ILE	I	I	147 - 186	149 - 188
10	2	GLU	GLU	GLY	GLY	J	J	147 - 189	149 - 191

NCS ensembles :

ID
1
2

Components

#1: Protein

A B C D E F G H I J
Putative rRNA methylase

Details:

Mass: 21837.955 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum ATCC 27405 (bacteria)
Gene: Cthe_0696 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DDA2

#2: Chemical

A-300 B-300 C-300 D-300 E-300 F-300 H-300 I-300 J-300
ChemComp-SAM / S-ADENOSYLMETHIONINE

Details:

Mass: 398.437 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S

#3: Chemical

A-301 A-302 A-303 B-301 C-301
ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄

#4: Chemical

A-304 B-302 F-301 H-301
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.53 ų/Da / Density % sol: 51.41 %
• Crystal grow: Temperature: 294 K / pH: 4.5 ; Details: 100MM SODIUM ACETATE, PH 4.5, 30% PEG8000, 200MM LITHIUM SULFATE, 10% GLYCEROL, 294K, pH 4.50

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
• Detector: Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2008 / Details: MIRRORS
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9791 Å / Relative weight: 1
• Reflection: Resolution: 2.2→50 Å / Num. obs: 109977 / % possible obs: 99.2 % / Observed criterion σ(I): -5 / Redundancy: 2.9 % / R_merge(I) obs: 0.081 / Net I/σ(I): 5.5
• Reflection shell: Resolution: 2.2→2.28 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.6 / Mean I/σ(I) obs: 0.8 / % possible all: 98.3

Processing

Software

Name	Version	Classification
SHELX		model building
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SHELX		phasing

Refinement

Method to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.922 / SU B: 9.604 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.27843	3256	3 %	RANDOM
Rwork	0.24361	-	-	-
obs	0.24468	105464	99.13 %	-

• 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: 55.003 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-4.25 Å2	0 Å2	1.23 Å2
2-	-	2.23 Å2	0 Å2
3-	-	-	2.43 Å2

Refinement step

Cycle: LAST / Resolution: 2.2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14565	0	292	360	15217

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	15292
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.176	1.989	20698
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.759	5	1931
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.908	25.863	655
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.138	15	2791
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.825	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	2422
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	11163
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.139	0.3	6277
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.291	0.5	10424
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.5	1096
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	0.177	0.3	45
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.189	0.5	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	4.509	2	9720
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	6.524	3	15323
X-RAY DIFFRACTION	r_scbond_it	7.309	3	6205
X-RAY DIFFRACTION	r_scangle_it	10.391	5	5346
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	899	medium positional	0.08	0.1
1	2	B	899	medium positional	0.06	0.1
1	3	C	899	medium positional	0.07	0.1
1	4	D	899	medium positional	0.06	0.1
1	5	E	899	medium positional	0.05	0.1
1	6	F	899	medium positional	0.07	0.1
1	7	G	899	medium positional	0.1	0.1
1	8	H	899	medium positional	0.07	0.1
1	9	I	899	medium positional	0.06	0.1
1	10	J	899	medium positional	0.07	0.1
2	1	A	289	medium positional	0.08	0.1
2	2	B	289	medium positional	0.07	0.1
2	3	C	289	medium positional	0.07	0.1
2	4	D	289	medium positional	0.07	0.1
2	5	E	289	medium positional	0.07	0.1
2	6	F	289	medium positional	0.07	0.1
2	7	G	289	medium positional	0.08	0.1
2	8	H	289	medium positional	0.07	0.1
2	9	I	289	medium positional	0.06	0.1
2	10	J	289	medium positional	0.08	0.1
1	1	A	899	medium thermal	3.65	5
1	2	B	899	medium thermal	4.36	5
1	3	C	899	medium thermal	2.85	5
1	4	D	899	medium thermal	2.91	5
1	5	E	899	medium thermal	2.14	5
1	6	F	899	medium thermal	2.56	5
1	7	G	899	medium thermal	3.58	5
1	8	H	899	medium thermal	3.52	5
1	9	I	899	medium thermal	3.69	5
1	10	J	899	medium thermal	3.98	5
2	1	A	289	medium thermal	3.46	5
2	2	B	289	medium thermal	5.01	5
2	3	C	289	medium thermal	3.77	5
2	4	D	289	medium thermal	3.79	5
2	5	E	289	medium thermal	3.66	5
2	6	F	289	medium thermal	3.09	5
2	7	G	289	medium thermal	4.06	5
2	8	H	289	medium thermal	3.82	5
2	9	I	289	medium thermal	4.07	5
2	10	J	289	medium thermal	4.29	5

LS refinement shell

Resolution: 2.2→2.256 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.409	228	-
Rwork	0.352	7485	-
obs	-	-	96.44 %