PDB-3o0n: Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 3o0n

Title

Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP and Adenosylcobalamin

Components

Ribonucleoside-diphosphate reductase

Ribonucleotide reductase

Keywords

OXIDOREDUCTASE / 10 alpha/beta barrel / adenosylcobalamin dependent /

ribonucleotide reductase / Reduction ribonucleotide 2'-OH position / EFFECTOR DTTP /

COENZYME B12

Function / homology

Function and homology information

cobalamin binding /

ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA biosynthetic process /

DNA replication /

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.95 Å

Authors

Larsson, K.-M. / Logan, D.T. / Nordlund, P.

Citation

Journal: Acs Chem.Biol. / Year: 2010
Title: Structural Basis for Adenosylcobalamin Activation in AdoCbl-Dependent Ribonucleotide Reductases.
Authors: Larsson, K.M. / Logan, D.T. / Nordlund, P.

History

Deposition	Jul 19, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 28, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 24, 2012	Group: Non-polymer description
Revision 1.3	Nov 8, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4	Jul 17, 2019	Group: Data collection / Refinement description / Category: software Item: _software.classification / _software.name / _software.version
Revision 1.5	Sep 6, 2023	Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3o0n.cif.gz	520.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o0/3o0n ftp://data.pdbj.org/pub/pdb/validation_reports/o0/3o0n	HTTPS FTP

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Related structure data

Related structure data	3o0oC 3o0qC 1xjeS 1xjf 1xjg 1xjj 1xjm 1xjn C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1xjm-d 3o0o-d 1xje-d 1xjj-d 1xjn-1 3o0q-d 1xjn-2 1xjf-d 1xjk-d 1xjg-d 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	#238 - Oct 2019 Ribonucleotide Reductase similarity (8) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: Ribonucleoside-diphosphate reductase

B: Ribonucleoside-diphosphate reductase

hetero molecules

149 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	119.010, 123.820, 106.440
Angle α, β, γ (deg.)	90.00, 103.10, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1004- CL

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Protein , 1 types, 2 molecules AB

#1: Protein	Ribonucleoside-diphosphate reductase / Ribonucleotide reductase Mass: 73374.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nrdJ, TM_0118 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O33839, ribonucleoside-diphosphate reductase

#1: Protein

Ribonucleoside-diphosphate reductase /

Ribonucleotide reductase

Mass: 73374.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermotoga maritima (bacteria) / Gene: nrdJ, TM_0118 / Plasmid: pET-22b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O33839,

ribonucleoside-diphosphate reductase

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Non-polymers , 7 types, 521 molecules

#2: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#3: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-B12 / COBALAMIN / Vitamin B12 Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆₂H₈₉CoN₁₃O₁₄P
#7: Chemical	ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₃
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	STUDIES SUGGEST A POINT MUTATION EITHER IN THE SEQUENCING CLONE (SER->TYR MUTATION) OR IN THEIR ...STUDIES SUGGEST A POINT MUTATION EITHER IN THE SEQUENCING CLONE (SER->TYR MUTATION) OR IN THEIR EXPRESSION CLONE (TYR->SER). CODONS FOR TYR=ATA AND SER=AGA.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 10% PEG8000, 0.1M sodium acetate, 0.1 M sodium chloride, 10mM DTT (dithiotreithol), 5% glycerol, crystallization geometry: 4 microL protein 11miligram/milliL + 2uL reservoir solution over ...Details: 10% PEG8000, 0.1M sodium acetate, 0.1 M sodium chloride, 10mM DTT (dithiotreithol), 5% glycerol, crystallization geometry: 4 microL protein 11miligram/milliL + 2uL reservoir solution over 300 microL in 24-well plate. Crystals in 3-4 days, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 2.6 Å³/Da / Density % sol: 52.74 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG8000, 0.1M sodium acetate, 0.1 M sodium chloride, 10mM DTT (dithiotreithol), 5% glycerol, crystallization geometry: 4 microL protein 11miligram/milliL + 2uL reservoir solution over ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 24, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 1.95→20 Å / Num. obs: 108100 / % possible obs: 99 % / Redundancy: 4.45 % / B_iso Wilson estimate: 30.5 Å² / R_merge(I) obs: 0.092 / R_sym value: 0.1019
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.088 / Mean I/σ(I) obs: 0.0159 / Num. unique all: 7919 / R_sym value: 0.805

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.6.2_432)	refinement
REFMAC		refinement
ProDC		data collection
XDS		data reduction
XSCALE		data scaling
REFMAC		phasing

Refinement

Method to determine structure: RIGID BODY REFINEMENT
Starting model: PDB entry 1XJE

1xje

Resolution: 1.95→19.97 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2493	5407	5 %
R_work	0.2025	-	-
obs	0.2049	108084	99.15 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 53.653 Å² / k_sol: 0.352 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.7239 Å²	-0 Å²	6.4507 Å²
2-	-	3.3735 Å²	0 Å²
3-	-	-	-6.0974 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→19.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9782	0	171	513	10466

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10157
X-RAY DIFFRACTION	f_angle_d	1.081	13764
X-RAY DIFFRACTION	f_dihedral_angle_d	15.178	3903
X-RAY DIFFRACTION	f_chiral_restr	0.071	1532
X-RAY DIFFRACTION	f_plane_restr	0.005	1748

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-1.9721	0.41	161	0.3852	3430	X-RAY DIFFRACTION	100
1.9721-1.9953	0.4125	192	0.3824	3438	X-RAY DIFFRACTION	100
1.9953-2.0196	0.4188	162	0.3727	3424	X-RAY DIFFRACTION	100
2.0196-2.0452	0.3849	170	0.3567	3468	X-RAY DIFFRACTION	100
2.0452-2.0721	0.4018	172	0.3599	3384	X-RAY DIFFRACTION	99
2.0721-2.1004	0.3672	163	0.3322	3521	X-RAY DIFFRACTION	100
2.1004-2.1304	0.3899	179	0.3204	3414	X-RAY DIFFRACTION	100
2.1304-2.1621	0.3511	188	0.3151	3411	X-RAY DIFFRACTION	100
2.1621-2.1959	0.3304	170	0.2899	3416	X-RAY DIFFRACTION	99
2.1959-2.2318	0.3586	173	0.2716	3410	X-RAY DIFFRACTION	99
2.2318-2.2703	0.3071	174	0.2711	3435	X-RAY DIFFRACTION	99
2.2703-2.3115	0.3176	190	0.2536	3399	X-RAY DIFFRACTION	99
2.3115-2.3559	0.3136	172	0.2465	3383	X-RAY DIFFRACTION	99
2.3559-2.4039	0.3068	181	0.2344	3429	X-RAY DIFFRACTION	99
2.4039-2.4561	0.3029	206	0.2389	3408	X-RAY DIFFRACTION	99
2.4561-2.5131	0.2824	173	0.2323	3391	X-RAY DIFFRACTION	99
2.5131-2.5758	0.3266	188	0.2278	3428	X-RAY DIFFRACTION	99
2.5758-2.6453	0.3074	193	0.2153	3375	X-RAY DIFFRACTION	99
2.6453-2.723	0.2538	193	0.2017	3419	X-RAY DIFFRACTION	99
2.723-2.8106	0.2731	192	0.2073	3427	X-RAY DIFFRACTION	99
2.8106-2.9108	0.2951	182	0.2055	3407	X-RAY DIFFRACTION	99
2.9108-3.027	0.2212	198	0.1904	3395	X-RAY DIFFRACTION	99
3.027-3.1642	0.2833	175	0.1882	3465	X-RAY DIFFRACTION	99
3.1642-3.3303	0.2548	176	0.1859	3427	X-RAY DIFFRACTION	99
3.3303-3.5379	0.1998	153	0.1755	3440	X-RAY DIFFRACTION	99
3.5379-3.8093	0.2291	177	0.1708	3439	X-RAY DIFFRACTION	99
3.8093-4.1895	0.1904	183	0.1485	3421	X-RAY DIFFRACTION	99
4.1895-4.7884	0.1669	182	0.1316	3442	X-RAY DIFFRACTION	99
4.7884-6.0055	0.1939	198	0.1551	3414	X-RAY DIFFRACTION	99
6.0055-19.9712	0.1791	191	0.1582	3433	X-RAY DIFFRACTION	97

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	1.4864	-0.3848	-0.6802	0.9069	-0.5098	0.8983	-0.1862	-0.7223	-0.2842	0.1003	0.1033	0.1355	-0.3079	0.3123	0.0951	0.5449	0.1241	0.0351	0.69	0.3597	0.3286	-83.4735	-75.9076	11.6355
2	1.683	-0.576	-0.9827	0.7408	0.2623	0.8743	0.1333	-0.8797	0.0785	-0.1131	0.0668	-0.0555	-0.1765	0.5405	-0.2027	0.2509	-0.1626	0.0374	0.6307	-0.0401	0.1547	-85.6482	-51.4973	7.6815
3	0.0041	-0.0215	-0.0131	0.1945	0.0952	0.0554	0.0201	0.0011	0.0147	0.0562	-0.0282	0.075	0.0172	0.0069	0.0055	1.1254	-0.0834	0.1234	0.9332	0.0029	1.065	-104.0669	-77.4063	10.3928
4	0.9496	-0.4408	-0.0937	0.2009	0.0369	0.0158	0.1551	-0.9173	-0.3063	0.1262	-0.0294	0.0894	0.0769	0.0559	-0.1587	-0.1041	-0.2858	-0.1169	0.5923	0.1651	0.1917	-108.0402	-59.2168	14.7286
5	0.9904	0.5932	0.0717	0.4209	0.1576	0.4404	0.1435	-0.0129	0.4451	-0.0197	-0.0678	0.1896	-0.4868	0.0541	-0.1999	0.5547	-0.0547	0.1164	0.0668	0.0161	0.2636	-78.8131	-28.6587	-46.9877
6	0.7221	0.1633	-0.1691	0.6283	0.1707	1.6029	-0.079	-0.0379	-0.0458	0.0013	0.0614	0.0588	0.148	0.1944	0.0368	0.3012	0.0411	0.1072	0.0133	0.0192	0.0948	-75.1143	-51.2447	-42.017
7	0.2145	0.1695	-0.0095	0.1495	0.0245	0.0871	0.0607	0.0448	0.2916	0.122	-0.1197	0.3191	-0.094	0.041	0.0108	0.5409	0.0045	0.1738	0.2981	0.2054	0.6939	-101.1649	-42.4966	-62.3328
8	0.3172	-0.1635	-0.1189	0.108	0.0686	0.4772	-0.1865	0.1301	-0.2171	-0.0754	0.076	0.0686	0.3933	-0.0041	0.0877	0.426	-0.0613	0.0655	0.1049	-0.0048	0.226	-88.9698	-60.6075	-56.0638

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:40)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 41:511)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 512:528)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 529:633)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 1:66)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 67:511)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 512:551)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 552:633)

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