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- PDB-6p9v: Crystal Structure of hMAT Mutant K289L -

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Basic information

Entry
Database: PDB / ID: 6p9v
TitleCrystal Structure of hMAT Mutant K289L
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE / Adenosyl transferase / AdoMet synthase / Natural Product Enzyme
Function / homology
Function and homology information


methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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.
Similarity search - Domain/homology
ADENOSINE / : / PYROPHOSPHATE 2- / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.051 Å
AuthorsMiller, M.D. / Xu, W. / Huber, T.D. / Clinger, J.A. / Liu, Y. / Thorson, J.S. / Phillips Jr., G.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115261 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM098248 United States
National Science Foundation (NSF, United States)STC 1231306 United States
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes.
Authors: Huber, T.D. / Clinger, J.A. / Liu, Y. / Xu, W. / Miller, M.D. / Phillips Jr., G.N. / Thorson, J.S.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _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_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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.ptnr1_label_seq_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_conn.ptnr2_symmetry
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3835
Polymers45,8761
Non-polymers5074
Water2,846158
1
A: S-adenosylmethionine synthase isoform type-2
hetero molecules

A: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,76510
Polymers91,7522
Non-polymers1,0138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8450 Å2
ΔGint-33 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.348, 94.624, 116.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II


Mass: 45875.949 Da / Num. of mol.: 1 / Mutation: K289L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Plasmid: pET28a
Details (production host): expression construct from Prof. Chunming Liu.
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P31153, methionine adenosyltransferase

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Non-polymers , 5 types, 162 molecules

#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M KCl, 0.05M HEPES, 35% (v/v) Pentaeythritol propoxylate (5/4 PO/OH), PROTEIN BUFFER ADDITIVES: 0.002M ADP, 0.005M magnesium chloride, 0.010M metol -- [(S)-(-)-methioninol]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 6, 2017
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.051→39.742 Å / Num. obs: 16840 / % possible obs: 72.01 % / Redundancy: 8.68 % / Biso Wilson estimate: 45.815 Å2
Details: Data were elliptically truncated with STARANISO. Statistics reported are for the observed reflections in spherical shells after apply the elliptical observation criterion. Elliptical ...Details: Data were elliptically truncated with STARANISO. Statistics reported are for the observed reflections in spherical shells after apply the elliptical observation criterion. Elliptical completeness is 94% overall and 82% in the high resolution shell.
CC1/2: 0.9963 / Rmerge(I) obs: 0.194 / Rrim(I) all: 0.207 / Χ2: 1.119 / Net I/σ(I): 9.29 / Num. measured all: 146211
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.423-39.74217.460.04730.74662758410.99680.0180.051
5.048-6.42318.280.06922.84969728420.99830.0260.074
4.39-5.04818.340.06824.50470248420.99740.0250.072
3.974-4.3918.530.08320.17971918430.99730.030.088
3.682-3.97418.580.11716.99772128410.99490.0420.124
3.458-3.68218.630.14913.51872798430.99370.0540.158
3.277-3.45818.80.19311.03674088420.99530.0680.205
3.131-3.27718.840.2648.62474338410.9920.0930.28
3.01-3.13118.870.3746.37574658420.98250.1320.397
2.901-3.010.99298.930.4835.11375218420.96050.1690.513
2.802-2.9010.91428.850.5734.30574508420.94670.2020.608
2.707-2.8020.84728.820.6293.91974328430.94420.2230.668
2.616-2.7070.77188.810.6883.61174208420.91890.2440.731
2.53-2.6160.7178.90.8152.96774858410.89470.2870.865
2.448-2.530.64828.910.9222.46875068420.76310.3270.979
2.367-2.4480.59038.981.0512.21675708430.75310.371.115
2.291-2.3670.5459.031.1871.9576068420.70090.4171.259
2.216-2.2910.48959.071.4031.74576368420.58050.4891.487
2.139-2.2160.40859.091.4771.60776548420.53380.5151.566
2.051-2.1390.30887.941.8611.1866728420.30230.6831.988

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSVERSION Jun 1, 2017 BUILT=20170923data reduction
XDSVERSION Jun 1, 2017 BUILT=20170923data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2P02

2p02


Resolution: 2.051→39.74 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.36 / Stereochemistry target values: ML
Details: 1. Data was aniostropically truncated with Staraniso. 2. Reference model restraints derrived from a higher resolution native structure, PDB-ID 2p02, were applied throughout. 3. While the ...Details: 1. Data was aniostropically truncated with Staraniso. 2. Reference model restraints derrived from a higher resolution native structure, PDB-ID 2p02, were applied throughout. 3. While the crystallization drop was setup with protein in a buffer containing 0.002M ADP, the density in the ATP binding site had a break indicating that it was likely adenosine and not ADP bound. The density in the region of the phosphate binding site was disordered. In the end, it was modeled as a disordered pyrophosphate with a magnesium ion from the protein buffer and a potassium ion from the crystallization condition.
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 825 4.9 %RANDOM
Rwork0.1726 16010 --
obs0.1741 16835 72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.94 Å2 / Biso mean: 40.9341 Å2 / Biso min: 5.54 Å2
Refinement stepCycle: final / Resolution: 2.051→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 69 158 3158
Biso mean--30.22 37.08 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023155
X-RAY DIFFRACTIONf_angle_d0.6424308
X-RAY DIFFRACTIONf_dihedral_angle_d11.2911929
X-RAY DIFFRACTIONf_chiral_restr0.048477
X-RAY DIFFRACTIONf_plane_restr0.004564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.051-2.17950.325580.2497121333
2.1795-2.34780.2508910.2225179949
2.3478-2.5840.24121020.2098231963
2.584-2.95780.2421670.1902312485
2.9578-3.72610.19781920.16193719100
3.7261-39.740.17452150.15443836100
Refinement TLS params.Method: refined / Origin x: 8.3014 Å / Origin y: 7.9366 Å / Origin z: 32.2543 Å
111213212223313233
T0.1783 Å2-0.034 Å20.0077 Å2-0.1289 Å20.0133 Å2--0.1513 Å2
L0.7535 °2-0.1176 °2-0.0769 °2-1.0158 °20.0115 °2--1.2797 °2
S-0.0315 Å °0.0422 Å °0.0332 Å °-0.0762 Å °0.0241 Å °-0.1209 Å °-0.0415 Å °0.0845 Å °0.0065 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 16 through 395)

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