PDB-7r2w: Mutant S-adenosylmethionine synthetase from E.coli complexed with...

Basic information

• Entry: Database: PDB / ID: 7r2w
• Title: Mutant S-adenosylmethionine synthetase from E.coli complexed with AMPPNP and methionine
• Components: S-adenosylmethionine synthase
• Keywords: TRANSFERASE / Dihedral D2 symmetry / homotetramer A4 symmetry / isologous interfaces 2 / S-adenosylmethionine synthetase

Function / homology

Function:

methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding / cytosol

Domain/homology:

GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2. / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta

Component:

PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / S-adenosylmethionine synthase

• Biological species: Escherichia coli (E. coli)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
• Authors: Shahar, A. / Kleiner, D. / Bershtein, S. / Zarivach, R.

Funding support

United States, 1items

Organization	Grant number	Country
United States - Israel Binational Science Foundation (BSF)	2020640	United States

• Citation: Journal: Protein Sci. / Year: 2022; Title: Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains.; Authors: Kleiner, D. / Shapiro Tuchman, Z. / Shmulevich, F. / Shahar, A. / Zarivach, R. / Kosloff, M. / Bershtein, S.

History

Deposition	Feb 6, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Assembly

Deposited unit

A: S-adenosylmethionine synthase

hetero molecules

Summary:

• 43.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	43,420	5
Polymers	42,826	1
Non-polymers	594	4
Water	3,333	185

1

A: S-adenosylmethionine synthase

hetero molecules

A: S-adenosylmethionine synthase

hetero molecules

A: S-adenosylmethionine synthase

hetero molecules

A: S-adenosylmethionine synthase

hetero molecules

Summary:

• defined by author&software
• Evidence: gel filtration
• 174 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	173,681	20
Polymers	171,306	4
Non-polymers	2,376	16
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_445	-x-1,-y-1,z	1
crystal symmetry operation	7_555	y,x,-z	1
crystal symmetry operation	8_445	-y-1,-x-1,-z	1

Calculated values:

Buried area	19820 Å2
ΔGint	-141 kcal/mol
Surface area	48260 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	86.611, 86.611, 90.982
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P42212

Components on special symmetry positions

ID	Model	Components
1	1	A-564- HOH
2	1	A-666- HOH
3	1	A-676- HOH

Components

#1: Protein

A S-adenosylmethionine synthase / AdoMet synthase / MAT / Methionine adenosyltransferase

Details:

Mass: 42826.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metK / Production host: Escherichia coli (E. coli) / References: UniProt: C3SV92, methionine adenosyltransferase

#2: Chemical

A-401 ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Details:

Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM

#3: Chemical

A-402 A-403 ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

A-404 ChemComp-K / POTASSIUM ION

Details:

Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 1.99 ų/Da / Density % sol: 38.25 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M L-Proline 0.1M Hepes pH 7.56 14% PEG 3350

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
• Detector: Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 26, 2021
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97626 Å / Relative weight: 1
• Reflection: Resolution: 1.6→62.73 Å / Num. obs: 46194 / % possible obs: 99.96 % / Redundancy: 45.8 % / B_iso Wilson estimate: 31.66 Ų / CC_1/2: 1 / R_rim(I) all: 0.083 / Net I/σ(I): 26.2
• Reflection shell: Resolution: 1.6→1.658 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4536 / CC_1/2: 0.4 / R_rim(I) all: 4.035

Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P7L

1p7l

Resolution: 1.6→62.73 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.961 / SU B: 5.327 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2196	2366	5.1 %	RANDOM
Rwork	0.18193	-	-	-
obs	0.18391	43830	99.97 %	-

• 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: 36.14 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.17 Å2	-0 Å2	0 Å2
2-	-	0.17 Å2	0 Å2
3-	-	-	-0.34 Å2

Refinement step

Cycle: 1 / Resolution: 1.6→62.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2895	0	34	185	3114

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	2993
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2802
X-RAY DIFFRACTION	r_angle_refined_deg	2.013	1.647	4065
X-RAY DIFFRACTION	r_angle_other_deg	1.512	1.58	6467
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.179	5	375
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.321	22.617	149
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.198	15	497
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.155	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	398
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3382
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	655
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	2.134	3.02	1500
X-RAY DIFFRACTION	r_mcbond_other	2.131	3.019	1499
X-RAY DIFFRACTION	r_mcangle_it	2.96	4.521	1872
X-RAY DIFFRACTION	r_mcangle_other	2.96	4.524	1873
X-RAY DIFFRACTION	r_scbond_it	3.084	3.445	1490
X-RAY DIFFRACTION	r_scbond_other	3.084	3.445	1490
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.652	5.031	2192
X-RAY DIFFRACTION	r_long_range_B_refined	6.236	36.024	3246
X-RAY DIFFRACTION	r_long_range_B_other	6.243	35.786	3221
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.6→1.642 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.313	181	-
Rwork	0.337	3159	-
obs	-	-	99.61 %

Refinement TLS params.

Method: refined / Origin x: -30.5058 Å / Origin y: -17.9372 Å / Origin z: -8.3582 Å

	11	12	13	21	22	23	31	32	33
T	0.0191 Å2	0.002 Å2	-0.0025 Å2	-	0.0254 Å2	0.0176 Å2	-	-	0.0148 Å2
L	0.5286 °2	0.238 °2	0.03 °2	-	0.6309 °2	0.0206 °2	-	-	0.6338 °2
S	-0.0437 Å °	0.09 Å °	0.0795 Å °	-0.0217 Å °	0.0455 Å °	0.0623 Å °	-0.069 Å °	0.0034 Å °	-0.0017 Å °