PDB-3fpj: Crystal Structure of E81Q mutant of MtNAS in complex with S-ADENO...

ID or keywords:

Entry

Database: PDB / ID: 3fpj

Title

Crystal Structure of E81Q mutant of MtNAS in complex with S-ADENOSYLMETHIONINE

Components

Putative uncharacterized protein

Keywords

BIOSYNTHETIC PROTEIN / TRANSFERASE / thermonicotianamine / nicotianamine

Function / homology

Function and homology information

nicotianamine synthase activity / nicotianamine biosynthetic process / identical protein binding
Similarity search - Function

Biological species

Methanothermobacter thermautotrophicus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Dreyfus, C. / Pignol, D. / Arnoux, P.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystallographic snapshots of iterative substrate translocations during nicotianamine synthesis in Archaea
Authors: Dreyfus, C. / Lemaire, D. / Mari, S. / Pignol, D. / Arnoux, P.

History

Deposition	Jan 5, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 10, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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	3fpj.cif.gz	135.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3fpj.ent.gz	103.5 KB	Display	PDB format
PDBx/mmJSON format	3fpj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3fpj_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	3fpj_full_validation.pdf.gz	1.2 MB	Display
Data in XML	3fpj_validation.xml.gz	30.9 KB	Display
Data in CIF	3fpj_validation.cif.gz	44.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fp/3fpj ftp://data.pdbj.org/pub/pdb/validation_reports/fp/3fpj	HTTPS FTP

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Related structure data

Related structure data	3fpeSC 3fpfC 3fpgC 3fphC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3fpg-d 3fph-d 3o31-d 3fpe-d 5veb-1 1q13-d 5cf2-d 4wby-d 4ci8-1 1vbj-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	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Putative uncharacterized protein

B: Putative uncharacterized protein

hetero molecules

69 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)	64.600, 68.980, 147.390
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative uncharacterized protein / MtNAS Mass: 33849.734 Da / Num. of mol.: 2 / Mutation: E81Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: MTH675 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O26771
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.43 Å³/Da / Density % sol: 49.29 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 22% PEG 3350, 400mM NaBr, pH 8, vapor diffusion, hanging drop, temperature 294K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-2 / Wavelength: 0.933 Å

Detector

Type: MARRESEARCH / Detector: CCD / Date: Sep 28, 2008

Radiation

Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.933 Å / Relative weight: 1

Reflection

Resolution: 1.8→29.801 Å / Num. all: 61834 / Num. obs: 61711 / % possible obs: 99.8 % / Redundancy: 4.7 % / R_merge(I) obs: 0.077 / R_sym value: 0.077 / Net I/σ(I): 5.95

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.8-1.9	4.8	0.376	1.9	42893	8937	0.376	100
1.9-2.01	4.7	0.291	1.8	39634	8460	0.291	99.7
2.01-2.15	4.8	0.128	5.5	38443	7954	0.128	100
2.15-2.32	4.6	0.179	2.5	33913	7357	0.179	99.6
2.32-2.55	4.8	0.076	8.7	33130	6867	0.076	100
2.55-2.85	4.8	0.06	10.8	29777	6205	0.06	100
2.85-3.29	4.8	0.048	12.4	26483	5536	0.048	100
3.29-4.02	4.7	0.05	10.8	22072	4680	0.05	99.8
4.02-5.69	4.6	0.042	12.1	17045	3670	0.042	99.6
5.69-29.8	4.2	0.032	17.9	8597	2045	0.032	96.5

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.25	data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FPE

3fpe

Resolution: 1.8→29.8 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.888 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.807 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.284	3082	5 %	RANDOM
R_work	0.225	-	-	-
obs	0.228	61502	99.43 %	-

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 max: 148.23 Å² / B_iso mean: 14.14 Å² / B_iso min: 2.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.38 Å²	0 Å²	0 Å²
2-	-	0.6 Å²	0 Å²
3-	-	-	-0.98 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4164	0	76	540	4780

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.027	0.022	4364
X-RAY DIFFRACTION	r_angle_refined_deg	2.506	1.99	5915
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	10.467	5	531
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.453	22.97	202
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.597	15	764
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.984	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.18	0.2	665
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3270
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	2396
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	2943
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.229	0.2	428
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.22	0.2	57
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.235	0.2	43
X-RAY DIFFRACTION	r_mcbond_it	1.375	1.5	2728
X-RAY DIFFRACTION	r_mcangle_it	1.865	2	4252
X-RAY DIFFRACTION	r_scbond_it	3.561	3	1907
X-RAY DIFFRACTION	r_scangle_it	4.915	4.5	1657

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.378	214	-
R_work	0.297	4315	-
all	-	4529	-
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	8.4267	0.5042	-3.5556	0.3413	-1.1948	4.6	-0.0221	0.0321	0.2463	0.0255	-0.0149	0.0801	0.2647	-0.0835	0.037	0.0103	-0.0116	0.0092	-0.0082	-0.0048	0.0151	5.3273	3.329	17.893
2	3.4498	0.5097	-1.5588	1.9778	-0.6076	7.4095	0.0608	0.6593	0.0177	0.0299	-0.0869	-0.1965	0.0992	0.5227	0.0261	0.0059	0.0607	-0.0724	0.0632	-0.0132	-0.0206	12.093	-2.6253	5.1251
3	4.0178	0.688	-0.3462	0.6986	0.1172	1.2544	0.1751	-0.0699	0.2131	0.1645	-0.0931	0.0468	0.0643	-0.0703	-0.082	0.0136	-0.0207	0.008	-0.0042	0.0058	0.0104	-2.5665	3.3034	13.354
4	0.5356	0.5127	-0.3232	3.5601	2.4521	2.9515	0.0127	0.0391	0.0213	0.0295	0.0274	-0.0587	-0.0065	0.1297	-0.0402	-0.0015	0.0334	-0.0142	0.0493	0.0234	-0.0006	8.7306	-5.1628	-9.3551
5	10.1751	-3.2259	4.3429	3.1121	-3.3086	5.3296	0.0195	-0.0978	-0.3016	-0.1602	0.3108	0.3309	0.242	-0.1962	-0.3303	0.0713	-0.0321	0.0034	-0.0124	0.0226	0.005	-9.4442	-9.9803	-7.9363
6	1.1579	-0.8813	0.1603	1.0259	-0.2984	1.5934	0.0386	0.0191	-0.0226	-0.0283	0.0204	-0.0256	0.057	0.0084	-0.059	0.0282	0.0015	-0.0035	0.0238	0.011	-0.0079	-4.4496	-0.3673	-19.0777
7	0.6695	-0.0004	0.1795	1.1099	-0.6216	1.6374	0.0348	0.0236	0.056	0.0791	0.1334	0.0953	-0.1401	-0.312	-0.1683	0.0089	0.0422	0.0289	0.0732	0.048	-0.0101	-12.9895	4.6647	-4.3563
8	17.4991	-4.3695	-13.8234	2.0786	0.777	18.1643	0.4809	0.6124	0.3568	-0.3062	-0.3356	0.0589	0.0906	0.4546	-0.1453	-0.0494	0.0396	-0.0093	0.1344	0.1073	-0.0542	-33.5321	6.4599	2.4619
9	3.5357	0.2798	0.3496	1.5851	-0.3954	0.4384	0.1151	0.161	0.0141	-0.1154	0.0101	0.053	0.0707	0.042	-0.1252	0.047	0.0105	-0.0218	0.0364	0.0122	0.0186	-38.7007	2.096	13.3299
10	25.4633	-5.0709	-16.1694	7.4082	8.0131	13.8582	-0.1967	0.4836	0.4183	-0.0068	-0.2007	-0.3616	0.0739	0.5132	0.3974	-0.0376	0.0129	0.0445	0.0138	0.199	0.0083	-26.9109	11.352	8.0444
11	2.1229	3.0663	-3.0134	5.9922	-6.0859	6.1993	0.037	-0.0338	0.0813	0.0985	-0.0482	0.0061	-0.1227	-0.0389	0.0111	-0.0046	0.0026	0.0042	-0.0115	0.0039	0.0183	-38.8637	1.793	23.4175
12	1.8833	0.3967	-0.278	0.7675	0.1364	1.1693	-0.0314	0.0179	-0.0553	-0.0296	0.0191	-0.0008	0.018	0.0021	0.0123	0.0886	0.0007	0.0027	-0.0126	0.0061	0.021	-32.6808	-14.731	28.3617
13	1.1385	0.2676	-0.1009	0.9347	0.1278	0.7223	-0.0266	-0.0328	-0.0293	0.0233	0.0153	0.0489	0.0414	-0.0023	0.0113	0.0477	-0.0031	0.004	0.0166	-0.0045	-0.0026	-28.0988	-7.8364	39.3063
14	0.8996	-0.1129	0.1893	0.7502	0.3549	1.5309	0.0477	0.0111	0.0753	0.0035	-0.0111	-0.0504	-0.0466	0.0901	-0.0366	0.0201	-0.0132	0.014	0.0197	0.0011	0.0212	-18.1591	0.3613	26.6972

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 19
2	X-RAY DIFFRACTION	2	A	20 - 39
3	X-RAY DIFFRACTION	3	A	40 - 70
4	X-RAY DIFFRACTION	4	A	71 - 103
5	X-RAY DIFFRACTION	5	A	104 - 121
6	X-RAY DIFFRACTION	6	A	122 - 191
7	X-RAY DIFFRACTION	7	A	192 - 265
8	X-RAY DIFFRACTION	8	B	2 - 12
9	X-RAY DIFFRACTION	9	B	13 - 54
10	X-RAY DIFFRACTION	10	B	55 - 63
11	X-RAY DIFFRACTION	11	B	64 - 86
12	X-RAY DIFFRACTION	12	B	87 - 121
13	X-RAY DIFFRACTION	13	B	122 - 193
14	X-RAY DIFFRACTION	14	B	194 - 266

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