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- PDB-1i7m: HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PY... -

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Basic information

Entry
Database: PDB / ID: 1i7m
TitleHUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE
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
4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE / 1,4-DIAMINOBUTANE / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 9, 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: Derived calculations / 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_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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 2.1Oct 9, 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
D: S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN
C: S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4958
Polymers77,8594
Non-polymers6374
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN
C: S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2484
Polymers38,9292
Non-polymers3182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-33 kcal/mol
Surface area12890 Å2
MethodPISA
3
B: S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN
A: S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2484
Polymers38,9292
Non-polymers3182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-27 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.899, 55.672, 96.086
Angle α, β, γ (deg.)90.00, 110.39, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe native enzyme is a dimer and the dimer is in the asymmetric unit.

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Components

#1: Protein S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN


Mass: 7741.471 Da / Num. of mol.: 2
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: 31187.805 Da / Num. of mol.: 2
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-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2
#4: Chemical ChemComp-CG / 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE


Mass: 230.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 %(w/w)PEG80001reservoir
2100 mMTris-HCl1reservoir
310 mMdithiothreitol1reservoir
42 mMprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.0402 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 1998
RadiationMonochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0402 Å / Relative weight: 1
ReflectionResolution: 2.24→30.715 Å / Num. all: 35553 / Num. obs: 34984 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 4.3
Reflection shellResolution: 2.24→2.39 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.2 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 86417
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→29.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 51995.74 / 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
Rfree0.294 3542 10.2 %RANDOM
Rwork0.242 ---
all-35568 --
obs-34785 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.96 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.92 Å20 Å2-0.14 Å2
2---5.95 Å20 Å2
3---12.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.24→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 46 243 5225
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 2.24→2.38 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 549 9.4 %
Rwork0.29 5269 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEINMAO.PARAMPROTEINMAO.TOP
X-RAY DIFFRACTION2ALL3.PARAMALL3.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.74
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: 0.337 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.29

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