PDB-4ckb: Vaccinia virus capping enzyme complexed with GTP and SAH

ID or keywords:

Entry

Database: PDB / ID: 4ckb

Title

Vaccinia virus capping enzyme complexed with GTP and SAH

Components

MRNA-CAPPING ENZYME CATALYTIC SUBUNIT
MRNA-CAPPING ENZYME REGULATORY SUBUNIT

Keywords

TRANSFERASE/HYDROLASE / TRANSFERASE-HYDROLASE COMPLEX / TRIFUNCTIONAL VACCINIA VIRUS MRNA CAPPING ENZYME

Function / homology

Function and homology information

inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / DNA-templated transcription termination / virion component / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...
Similarity search - Function

Biological species

VACCINIA VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Kyrieleis, O.J.P. / Chang, J. / de la Pena, M. / Shuman, S. / Cusack, S.

Citation

Journal: Structure / Year: 2014
Title: Crystal Structure of Vaccinia Virus Mrna Capping Enzyme Provides Insights Into the Mechanism and Evolution of the Capping Apparatus.
Authors: Kyrieleis, O.J.P. / Chang, J. / De La Pena, M. / Shuman, S. / Cusack, S.

History

Deposition	Jan 2, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ckb.cif.gz	894.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ckb.ent.gz	742.9 KB	Display	PDB format
PDBx/mmJSON format	4ckb.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/ck/4ckb ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4ckb	HTTPS FTP

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Related structure data

Related structure data	4ckcC 4ckeC 2vdwS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4cke-2 4cke-1 4ckc-2 4ckc-1 3wql-d 2xvi-d 1j3n-2 2ykv-d 3pvz-d 2xvj-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (7) #103 - Jul 2008 Dengue Virus similarity (1) #197 - May 2016 Zika Virus similarity (1)

Deposited unit

A: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT

B: MRNA-CAPPING ENZYME REGULATORY SUBUNIT

D: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT

E: MRNA-CAPPING ENZYME REGULATORY SUBUNIT

hetero molecules

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

1

D: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT

E: MRNA-CAPPING ENZYME REGULATORY SUBUNIT

hetero molecules

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

2

A: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT

B: MRNA-CAPPING ENZYME REGULATORY SUBUNIT

hetero molecules

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

Unit cell

Length a, b, c (Å)	60.340, 197.730, 61.110
Angle α, β, γ (deg.)	90.13, 109.27, 94.05
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	D
1	2	A
2	2	D
1	3	A
2	3	D
1	4	B
2	4	E

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 197
2	1	1	1	D	1 - 197
1	2	1	1	A	204 - 221
2	2	1	1	D	204 - 221
1	1	2	2	A	222 - 320
2	1	2	2	D	222 - 320
1	2	2	2	A	324 - 407
2	2	2	2	D	324 - 407
1	3	2	2	A	413 - 527
2	3	2	2	D	413 - 527
1	1	3	1	A	544 - 728
2	1	3	1	D	544 - 728
1	2	3	1	A	735 - 844
2	2	3	1	D	735 - 844
1	1	4	1	B	1 - 287
2	1	4	1	E	1 - 287

NCS ensembles :

ID
1
2
3
4

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.986259, -0.164926, 0.009643), (-0.164909, 0.986306, 0.002518), (-0.009926, 0.000893, -0.99995)	-60.19046, 89.11481, 18.4209
3	given	(1), (1), (1)
4	given	(-0.986536, -0.163521, 0.002881), (-0.163523, 0.986539, -0.000399), (-0.002777, -0.000864, -0.999996)	-60.11407, 89.28198, 18.62575
5	given	(1), (1), (1)
6	given	(-0.992491, -0.122202, -0.005247), (-0.12223, 0.992488, 0.00522), (0.004569, 0.005822, -0.999973)	-57.46082, 91.51631, 19.42024
7	given	(1), (1), (1)
8	given	(-0.991299, -0.131421, 0.007444), (-0.131426, 0.991326, -0.00016), (-0.007358, -0.001137, -0.999972)	-58.36908, 90.97787, 18.37049

#1: Protein	MRNA-CAPPING ENZYME CATALYTIC SUBUNIT / VIRUS TERMINATION FACTOR LARGE SUBUNIT / VTF LARGE SUBUNIT / MRNA-CAPPING ENZYME 97 KDA SUBUNIT / ...VIRUS TERMINATION FACTOR LARGE SUBUNIT / VTF LARGE SUBUNIT / MRNA-CAPPING ENZYME 97 KDA SUBUNIT / MRNA-CAPPING ENZYME D1 SUBUNIT / MRNA-CAPPING ENZYME LARGE SUBUNIT / POLYNUCLEOTIDE 5'-TRIPHOSPHATASE / MRNA 5'-TRIPHOSPHATASE / TPASE / MRNA GUANYLYLTRANSFERASE / GTP--RNA GUANYLYLTRANSFERASE / GTASE / MRNA (GUANINE-N(7)-)-METHYLTRANSFERASE / MRNA CAP METHYLTRANSFERASE Mass: 96856.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VACCINIA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS References: UniProt: P04298, polynucleotide 5'-phosphatase, mRNA guanylyltransferase, mRNA (guanine-N7)-methyltransferase
#2: Protein	MRNA-CAPPING ENZYME REGULATORY SUBUNIT / VIRUS TERMINATION FACTOR SMALL SUBUNIT / VTF SMALL SUBUNIT / MRNA-CAPPING ENZYME 33 KDA SUBUNIT / ...VIRUS TERMINATION FACTOR SMALL SUBUNIT / VTF SMALL SUBUNIT / MRNA-CAPPING ENZYME 33 KDA SUBUNIT / MRNA-CAPPING ENZYME D12 SUBUNIT / MRNA-CAPPING ENZYME SMALL SUBUNIT Mass: 33396.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VACCINIA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS / References: UniProt: P04318
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#4: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.7 Å³/Da / Density % sol: 54.4 % / Description: NONE
Crystal grow	pH: 6.5 Details: PROTEIN SOLUTION AT 4 MG/ML IN 40 MM TRIS-HCL, PH 8.0, 200 MM NACL, 5 MM DTT WITH 100 MM GTP, 5 MM MANGANESE CHLORIDE, AND 5 MM ADOMET. RESERVOIR SOLUTION 0.1 M CITRIC ACID, PH 6.5, 1.2 M LICL, 6% PEG6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. obs: 62966 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.37 % / R_merge(I) obs: 0.08 / Net I/σ(I): 10.75
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 2.31 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 1.43 / % possible all: 90.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VDW

2vdw

Resolution: 2.8→49.2 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.905 / SU B: 44.995 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25477	3184	5.1 %	RANDOM
R_work	0.20889	-	-	-
obs	0.21118	59782	96.57 %	-

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: 76.694 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.09 Å²	-0.98 Å²	3.06 Å²
2-	-	-4.25 Å²	-0.64 Å²
3-	-	-	-0.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→49.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17754	0	84	25	17863

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	18193
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	17671
X-RAY DIFFRACTION	r_angle_refined_deg	1.126	1.976	24596
X-RAY DIFFRACTION	r_angle_other_deg	0.7	3	40744
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.217	5	2176
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.238	24.375	816
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.935	15	3372
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.359	15	92
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	2816
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	20011
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4065
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	1.915	4.538	8755
X-RAY DIFFRACTION	r_mcbond_other	1.915	4.538	8754
X-RAY DIFFRACTION	r_mcangle_it	3.347	6.797	10914
X-RAY DIFFRACTION	r_mcangle_other	3.347	6.797	10915
X-RAY DIFFRACTION	r_scbond_it	1.735	4.705	9438
X-RAY DIFFRACTION	r_scbond_other	1.731	4.698	9426
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.076	6.962	13663
X-RAY DIFFRACTION	r_long_range_B_refined	5.572	34.973	20022
X-RAY DIFFRACTION	r_long_range_B_other	5.556	34.95	20015
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
2	1	A	3027	medium positional	0.02	0.5
2	2	D	3027	medium positional	0.02	0.5
1	1	A	3377	tight thermal	14.48	0.5
1	2	D	3377	tight thermal	14.48	0.5
2	1	A	1744	tight thermal	12.43	0.5
2	2	D	1744	tight thermal	12.43	0.5
3	1	A	4587	tight thermal	7.25	0.5
3	2	D	4587	tight thermal	7.25	0.5
4	1	B	4630	tight thermal	15.43	0.5
4	2	E	4630	tight thermal	15.43	0.5
2	1	A	3027	medium thermal	12.61	2
2	2	D	3027	medium thermal	12.61	2

LS refinement shell

Resolution: 2.804→2.877 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.427	212	-
R_work	0.364	4316	-
obs	-	-	93.92 %

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	0.5045	0.4453	0.4465	1.4771	0.82	0.6033	-0.1143	0.0363	0.0273	0.2858	0.0675	0.1266	-0.0909	-0	0.0468	0.7276	0.1032	0.2152	0.1109	-0.0815	0.2315	-14.297	68.703	20.045
2	1.5373	0.0355	0.4533	0.2652	-0.46	1.2409	0.0185	0.0389	0.0704	-0.1183	-0.0685	-0.0177	-0.0169	0.0286	0.0501	0.2935	0.0252	-0.0201	0.3198	0.0783	0.3349	-41.841	-27.643	-1.313
3	0.5533	0.0944	0.0491	1.0574	0.307	0.5883	0.1721	0.102	0.057	-0.2308	-0.0408	0.0137	-0.0648	-0.0696	-0.1313	0.5544	0.0251	0.0645	0.1314	0.0027	0.212	-15.529	49.792	-6.266
4	0.1377	0.0626	-0.3794	1.6199	-0.2577	1.8043	0.0885	-0.0442	-0.1035	-0.0158	-0.0028	-0.0563	-0.3283	0.165	-0.0856	0.3099	-0.0501	-0.0041	0.3573	-0.0266	0.2661	-2.48	17.555	9.584
5	0.4104	-0.462	-0.7842	1.4512	0.4908	1.9941	-0.1572	0.0954	-0.1919	0.1525	-0.2598	0.2312	0.0259	-0.0608	0.417	0.3458	-0.1036	0.1407	0.1556	-0.0755	0.4179	-45.566	-80.167	9.18
6	1.6418	-0.0763	0.0482	0.405	-0.3552	0.5785	0.0742	-0.196	-0.1506	0.0446	-0.0523	0.0142	-0.0386	0.0369	-0.0219	0.216	-0.012	-0.0513	0.364	0.026	0.3408	-37.423	-46.196	24.944
7	1.8642	-1.058	-0.2901	1.2461	-0.429	0.8986	-0.0413	0.0934	-0.1101	0.073	0.0102	-0.0335	-0.0484	-0.172	0.0311	0.254	0.0342	-0.0486	0.404	-0.0166	0.2477	-21.733	-2.147	27.539
8	0.7378	0.3796	-0.2338	2.0691	0.8552	1.2512	0.0625	-0.1112	0.172	-0.1174	-0.203	-0.1102	0.2187	0.3059	0.1405	0.415	0.0403	0.2821	0.2746	0.0708	0.3311	-24.146	-97.131	-8.895

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 221
2	X-RAY DIFFRACTION	2	D	1 - 221
3	X-RAY DIFFRACTION	3	A	222 - 528
4	X-RAY DIFFRACTION	4	A	544 - 844
5	X-RAY DIFFRACTION	4	A	1845
6	X-RAY DIFFRACTION	5	D	544 - 844
7	X-RAY DIFFRACTION	5	D	1845
8	X-RAY DIFFRACTION	6	D	222 - 528
9	X-RAY DIFFRACTION	6	D	1846
10	X-RAY DIFFRACTION	7	B	1 - 287
11	X-RAY DIFFRACTION	8	E	1 - 287

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