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- PDB-1i79: HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PY... -

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Basic information

Entry
Database: PDB / ID: 1i79
TitleHUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND 5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE
Components
  • S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN
  • S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN
KeywordsLYASE / Spermidine biosynthesis / Decarboxylase / Pyruvate / S-ADENOSYLMETHIONINE / SANDWICH / ALLOSTERIC ENZYME / PYRUVOYL
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-MHZ / 1,4-DIAMINOBUTANE / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsTolbert, W.D. / Ekstrom, J.L. / Mathews, I.I. / Secrist III, J.A. / Pegg, A.E. / Ealick, S.E.
Citation
Journal: Biochemistry / Year: 2001
Title: The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase.
Authors: Tolbert, W.D. / Ekstrom, J.L. / Mathews, I.I. / Secrist III, J.A. / Kapoor, P. / Pegg, A.E. / Ealick, S.E.
#1: Journal: Structure / Year: 1999
Title: The Crystal Structure of Human S-adenosylmethionine Decarboxylase at 2.25 A Resolution Reveals a Novel Fold
Authors: Ekstrom, J.L. / Mathews, I.I. / Stanley, B.A. / Pegg, A.E. / Ealick, S.E.
History
DepositionMar 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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

Downloads & links

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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)38,8074
Polymers38,3672
Non-polymers4412
Water2,882160
1
B: S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN
A: S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN
hetero molecules

B: S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN
A: S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6148
Polymers76,7334
Non-polymers8814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)100.282, 50.751, 68.624
Angle α, β, γ (deg.)90.00, 105.27, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe native enzyme is a dimer generated by the crystallographic two-fold.

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Components

#1: Protein 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) / Production host: Escherichia coli (E. coli)
References: UniProt: P17707, adenosylmethionine decarboxylase
#2: Protein S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN


Mass: 30671.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P17707, adenosylmethionine decarboxylase
#3: Chemical ChemComp-MHZ / 5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE


Mass: 352.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24N8O3
#4: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 43.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Tris-HCl pH 8.0, dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 %(w/w)PEG80001reservoir
2100 mMTris-HCl1reservoir
310 mMdithiothreitol1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2000
RadiationMonochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.01→100 Å / Num. all: 22266 / Num. obs: 21309 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.3
Reflection shellResolution: 2.01→2.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.4 / % possible all: 95.3
Reflection
*PLUS
Num. measured all: 78987
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→25.38 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 987574.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2045 9.8 %RANDOM
Rwork0.212 ---
all0.228 22360 --
obs-20787 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.12 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-3.98 Å20 Å2-1.8 Å2
2--2.52 Å20 Å2
3----6.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.01→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 31 160 2724
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it2.061.5
X-RAY DIFFRACTIONc_mcangle_it3.172
X-RAY DIFFRACTIONc_scbond_it2.782
X-RAY DIFFRACTIONc_scangle_it3.972.5
LS refinement shellResolution: 2.01→2.14 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 324 10 %
Rwork0.278 2932 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEINMAO.PARAMPROTEINMAO.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.326 / % reflection Rfree: 10 % / Rfactor Rwork: 0.278

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