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- PDB-6c07: Crystal Structure of S-Adenosylmethionine synthetase (MetK/Mat) f... -

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Basic information

Entry
Database: PDB / ID: 6c07
TitleCrystal Structure of S-Adenosylmethionine synthetase (MetK/Mat) from Cryptosporidium parvum
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / S-Adenosylmethionine synthetase / Enzyme metabolism / Anti-infective target / Anti-cancer target
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / ATP binding / metal ion binding
Similarity search - Function
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 ...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
Similarity search - Domain/homology
: / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsOhren, J.F. / Viola, R.E.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Structure of a critical metabolic enzyme: S-adenosylmethionine synthetase from Cryptosporidium parvum.
Authors: Ohren, J. / Parungao, G.G. / Viola, R.E.
History
DepositionDec 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...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 / struct_conn
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,86414
Polymers179,5844
Non-polymers28010
Water21,6361201
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.390, 62.060, 191.583
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.063677, -0.008677, 0.997933), (-0.00012, -0.999962, -0.008687), (0.997971, 0.000433, -0.063675)6.73601, -72.145462, -7.81477
3given(1), (1), (1)
4given(0.075671, -0.015235, 0.997016), (0.004709, -0.999867, -0.015636), (0.997122, 0.005878, -0.075589)7.00602, -72.055023, -7.6037

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Components

#1: Protein
S-adenosylmethionine synthase


Mass: 44896.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd7_2650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5CYE4, methionine adenosyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1201 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.2 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03315 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 1.85→59.05 Å / Num. obs: 185005 / % possible obs: 98.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 25.34 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.05477 / Rpim(I) all: 0.05477 / Rrim(I) all: 0.07745 / Net I/av σ(I): 8.15 / Net I/σ(I): 8.15
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.5238 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 12821 / CC1/2: 0.532 / Rpim(I) all: 0.5238 / Rrim(I) all: 0.7408 / % possible all: 94.92

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.627
Highest resolutionLowest resolution
Rotation57.95 Å1.84 Å
Translation57.95 Å1.84 Å

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimless0.3.8data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ODJ

4odj


Resolution: 1.85→19.988 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.99
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 6388 5.02 %RANDOM
Rwork0.1573 ---
obs0.1596 127368 94.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11337 0 10 1201 12548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111644
X-RAY DIFFRACTIONf_angle_d1.0915763
X-RAY DIFFRACTIONf_dihedral_angle_d11.6766976
X-RAY DIFFRACTIONf_chiral_restr0.0631803
X-RAY DIFFRACTIONf_plane_restr0.0082038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.35051790.28254109X-RAY DIFFRACTION95
1.871-1.8930.271860.26684033X-RAY DIFFRACTION96
1.893-1.91610.29592270.25113965X-RAY DIFFRACTION94
1.9161-1.94030.29052280.24814023X-RAY DIFFRACTION94
1.9403-1.96580.28912110.23574040X-RAY DIFFRACTION96
1.9658-1.99270.26352170.23144092X-RAY DIFFRACTION96
1.9927-2.02120.28792150.2293971X-RAY DIFFRACTION95
2.0212-2.05130.26552180.2124067X-RAY DIFFRACTION96
2.0513-2.08330.24992160.2044136X-RAY DIFFRACTION97
2.0833-2.11740.26732350.19154073X-RAY DIFFRACTION97
2.1174-2.15390.24362210.1874100X-RAY DIFFRACTION96
2.1539-2.1930.2222410.18034062X-RAY DIFFRACTION97
2.193-2.23520.23112210.16534098X-RAY DIFFRACTION96
2.2352-2.28070.20272590.16014062X-RAY DIFFRACTION96
2.2807-2.33020.19912280.15324069X-RAY DIFFRACTION96
2.3302-2.38440.2051960.15334054X-RAY DIFFRACTION95
2.3844-2.44390.20381800.15063983X-RAY DIFFRACTION93
2.4439-2.50980.19632300.15194035X-RAY DIFFRACTION95
2.5098-2.58360.20851970.15374050X-RAY DIFFRACTION94
2.5836-2.66680.19662070.15113981X-RAY DIFFRACTION94
2.6668-2.76180.20512150.15024070X-RAY DIFFRACTION95
2.7618-2.87210.20372120.15534067X-RAY DIFFRACTION95
2.8721-3.00240.1962230.14524021X-RAY DIFFRACTION94
3.0024-3.16010.20642480.14823983X-RAY DIFFRACTION94
3.1601-3.35730.19481970.1443952X-RAY DIFFRACTION92
3.3573-3.61510.15952140.13423933X-RAY DIFFRACTION91
3.6151-3.97630.16982000.12013942X-RAY DIFFRACTION91
3.9763-4.54570.14381750.11384028X-RAY DIFFRACTION93
4.5457-5.7050.16111950.12484004X-RAY DIFFRACTION91
5.705-19.98950.2251970.18533977X-RAY DIFFRACTION89

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