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- PDB-3ep7: Human AdoMetDC E256Q mutant complexed with S-Adenosylmethionine m... -

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Basic information

Entry
Database: PDB / ID: 3ep7
TitleHuman AdoMetDC E256Q mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound
Components
  • S-adenosylmethionine decarboxylase alpha chain
  • S-adenosylmethionine decarboxylase beta chain
KeywordsLYASE / AdoMetDC with mutation in putrescine binding site / 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
PYRUVIC ACID / S-ADENOSYLMETHIONINE METHYL ESTER / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBale, S. / Lopez, M.M. / Makhatadze, G.I. / Fang, Q. / Pegg, A.E. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2008
Title: Structural Basis for Putrescine Activation of Human S-Adenosylmethionine Decarboxylase.
Authors: Bale, S. / Lopez, M.M. / Makhatadze, G.I. / Fang, Q. / Pegg, A.E. / Ealick, S.E.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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 / 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

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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)38,0844
Polymers37,5822
Non-polymers5032
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-38 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.439, 50.082, 70.174
Angle α, β, γ (deg.)90.000, 105.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 7694.577 Da / Num. of mol.: 1 / Fragment: UNP residues 1-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE-C145S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P17707, adenosylmethionine decarboxylase
#2: Protein S-adenosylmethionine decarboxylase alpha chain / AdoMetDC / SamDC


Mass: 29887.234 Da / Num. of mol.: 1 / Fragment: UNP residues 69-328 / Mutation: E256Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE-C145S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P17707, adenosylmethionine decarboxylase
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-SMM / S-ADENOSYLMETHIONINE METHYL ESTER


Mass: 414.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
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: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 18180 / Num. obs: 17373 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 4.8 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Χ2: 1.379 / Net I/σ(I): 9.943
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1560 / Rsym value: 0.256 / Χ2: 0.997 / % possible all: 72.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I7B

1i7b


Resolution: 2→39.14 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 158000 / 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
Rfree0.251 845 4.9 %RANDOM
Rwork0.226 ---
all0.226 18180 --
obs0.226 17373 80.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.886 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 86.58 Å2 / Biso mean: 35.781 Å2 / Biso min: 16.04 Å2
Baniso -1Baniso -2Baniso -3
1--7.16 Å20 Å2-1.84 Å2
2--19.74 Å20 Å2
3----12.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 32 186 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.56
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 112 4.7 %
Rwork0.307 2270 -
all-2382 -
obs-1560 66.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2pvl.parampvl.top
X-RAY DIFFRACTION3smm.paramsmm.top
X-RAY DIFFRACTION4water.param

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