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- PDB-1jen: HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE -

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Basic information

Entry
Database: PDB / ID: 1jen
TitleHUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE
Components
  • PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (ALPHA CHAIN))
  • PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (BETA CHAIN))
KeywordsS-ADENOSYLMETHIONINE DECARBOXYLASE / PYRUVOYL / GENE DUPLICATION / POLYAMINE BIOSYNTHESIS / SANDWICH / ALLOSTERIC ENZYME
Function / homology
Function and homology information


spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / putrescine binding / polyamine metabolic process / 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
S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsEkstrom, J.L. / Mathews, I.I. / Stanley, B.A. / Pegg, A.E. / Ealick, S.E.
CitationJournal: Structure Fold.Des. / 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
DepositionFeb 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (BETA CHAIN))
A: PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (ALPHA CHAIN))
D: PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (BETA CHAIN))
C: PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (ALPHA CHAIN))


Theoretical massNumber of molelcules
Total (without water)76,9334
Polymers76,9334
Non-polymers00
Water7,458414
1
B: PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (BETA CHAIN))
A: PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (ALPHA CHAIN))


Theoretical massNumber of molelcules
Total (without water)38,4672
Polymers38,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (BETA CHAIN))
C: PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (ALPHA CHAIN))


Theoretical massNumber of molelcules
Total (without water)38,4672
Polymers38,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.600, 55.800, 90.100
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998116, 0.057715, 0.020825), (0.050397, 0.964757, -0.258273), (-0.034997, -0.256737, -0.965847)
Vector: 89.2757, -7.2915, -37.1434)

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Components

#1: Protein PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (BETA CHAIN)) / ADOMETDC / SAMDC


Mass: 7694.577 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 PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (ALPHA CHAIN)) / ADOMETDC / SAMDC


Mass: 30772.105 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.3 Å3/Da / Density % sol: 49 % / Description: 22 SELENIUM ATOMS LOCATED IN ASYMMETRIC UNIT
Crystal growpH: 8 / Details: 12 - 16% PEG 8K, 10 MM TRIS-HCL, PH 8.0, pH 8.00
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-16 %PEG80001reservoir
210 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9791,0.9788,0.954
DetectorType: BRANDEIS / Detector: CCD / Date: Sep 1, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97881
30.9541
ReflectionResolution: 2.25→20 Å / Num. obs: 169725 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 15.95 Å2 / Rsym value: 0.05 / Net I/σ(I): 23.71
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 15 / Rsym value: 0.094 / % possible all: 98.1
Reflection
*PLUS
Num. obs: 33426 / % possible obs: 98.9 % / Num. measured all: 169725 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.094

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Processing

Software
NameVersionClassification
SnBphasing
SOLVEphasing
MLPHAREphasing
DMmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1571 5 %RANDOM
Rwork0.177 ---
obs-31619 98.9 %-
Displacement parametersBiso mean: 20.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 0 414 5333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.25→2.35 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2602 192 5 %
Rwork0.2255 3476 -
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19
LS refinement shell
*PLUS
Rfactor obs: 0.2255

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