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- PDB-3dz4: Human AdoMetDC with 5'-[(2-carboxamidoethyl)methylamino]-5'-deoxy... -

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Basic information

Entry
Database: PDB / ID: 3dz4
TitleHuman AdoMetDC with 5'-[(2-carboxamidoethyl)methylamino]-5'-deoxy-8-methyladenosine
Components
  • S-adenosylmethionine decarboxylase alpha chain
  • S-adenosylmethionine decarboxylase beta chain
KeywordsLYASE / Complexes of AdoMetDC with 8-substituted ligands / Decarboxylase / Pyruvate / S-adenosyl-L-methionine / Spermidine biosynthesis / Zymogen
Function / homology
Function and homology information


spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / putrescine binding / spermidine biosynthetic process / identical protein binding / cytosol
Similarity search - Function
S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 ...S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C8M / 1,4-DIAMINOBUTANE / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.84 Å
AuthorsBale, S. / McCloskey, D.E. / Pegg, A.E. / Secrist III, J.A. / Guida, W.C. / Ealick, S.E.
CitationJournal: J.Med.Chem. / Year: 2009
Title: New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C8 Substitution in Structural Analogues of S-Adenosylmethionine
Authors: McCloskey, D.E. / Bale, S. / Secrist III, J.A. / Tiwari, A. / Moss III, T.H. / Valiyaveettil, J. / Brooks, W.H. / Guida, W.C. / Pegg, A.E. / Ealick, S.E.
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: S-adenosylmethionine decarboxylase beta chain
A: S-adenosylmethionine decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8344
Polymers38,3812
Non-polymers4542
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-40 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.818, 50.949, 68.985
Angle α, β, γ (deg.)90.000, 105.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein S-adenosylmethionine decarboxylase beta chain / AdoMetDC / SamDC / S-adenosylmethionine decarboxylase alpha chain / S-adenosylmethionine ...AdoMetDC / SamDC / S-adenosylmethionine decarboxylase alpha chain / S-adenosylmethionine decarboxylase beta chain


Mass: 7694.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P17707, adenosylmethionine decarboxylase
#2: Protein S-adenosylmethionine decarboxylase alpha chain / AdoMetDC / SamDC / S-adenosylmethionine decarboxylase alpha chain / S-adenosylmethionine ...AdoMetDC / SamDC / S-adenosylmethionine decarboxylase alpha chain / S-adenosylmethionine decarboxylase beta chain


Mass: 30685.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P17707, adenosylmethionine decarboxylase
#3: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2
#4: Chemical ChemComp-C8M / 3-[{[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)amino]propanamid e / 5'-[(2-carboxamidomethyl)methylamino]-5'-deoxy-8-methyladenosine


Mass: 365.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG 8000, 100 mM Tris, 10 mM DTT, pH 8.0, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 28243 / Num. obs: 27656 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Χ2: 1.283 / Net I/σ(I): 17.4
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 8 / Num. unique all: 2724 / Rsym value: 0.14 / Χ2: 1.284 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
CNSphasing
RefinementStarting model: 1I7B.pdb

1i7b


Resolution: 1.84→45.11 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 218874 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1337 4.8 %RANDOM
Rwork0.204 ---
all0.204 28243 --
obs0.204 27656 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.076 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 77.83 Å2 / Biso mean: 26.542 Å2 / Biso min: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1-10.65 Å20 Å2-3.2 Å2
2---2.42 Å20 Å2
3----8.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 32 222 2748
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 209 5.1 %
Rwork0.229 3920 -
all-4129 -
obs-2724 84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2pyruvoyl.parampyruvoyl.top
X-RAY DIFFRACTION3map.parammap.top
X-RAY DIFFRACTION4water.param

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