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- PDB-9pbb: 293K human S-adenosylmethionine decarboxylase -

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Basic information

Entry
Database: PDB / ID: 9pbb
Title293K human S-adenosylmethionine decarboxylase
Components
  • S-adenosylmethionine decarboxylase alpha chain
  • S-adenosylmethionine decarboxylase beta chain
KeywordsLYASE / polyamine biosynthesis / decarboxylase / AdoMet
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, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase, core
Similarity search - Domain/homology
1,4-DIAMINOBUTANE / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsPatel, J.R. / Bonzon, T.J. / Bahkt, T. / Fagbohun, O.O. / Clinger, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR220081 United States
CitationJournal: Biomolecules / Year: 2025
Title: Multi-Temperature Crystallography of S-Adenosylmethionine Decarboxylase Observes Dynamic Loop Motions
Authors: Patel, J.R. / Bonzon, T.J. / Bakht, T.F. / Fagbohun, O.O. / Clinger, J.A.
History
DepositionJun 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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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)40,2724
Polymers40,0612
Non-polymers2102
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-39 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.418, 45.876, 72.248
Angle α, β, γ (deg.)90.000, 104.971, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein S-adenosylmethionine decarboxylase beta chain


Mass: 9375.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P17707
#2: Protein S-adenosylmethionine decarboxylase alpha 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 / Cell (production host): pET / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P17707
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.07 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 4mg/mL enzyme in 200mM NaCl 50mM HEPES pH 7.5 1:1 to reservoir solution containing 4-8% PEG 8000 and 50mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.16→37.41 Å / Num. obs: 16461 / % possible obs: 98.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.14 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.306 / Rpim(I) all: 0.123 / Rrim(I) all: 0.331 / Net I/σ(I): 5.1
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 706 / CC1/2: 0.285 / Rpim(I) all: 0.676 / Rrim(I) all: 1.2 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
xia2data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→37.41 Å / SU ML: 0.2291 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 815 5.01 %
Rwork0.208 15438 -
obs0.2088 16253 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.11 Å2
Refinement stepCycle: LAST / Resolution: 2.17→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 19 133 2613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752553
X-RAY DIFFRACTIONf_angle_d0.93373447
X-RAY DIFFRACTIONf_chiral_restr0.1022374
X-RAY DIFFRACTIONf_plane_restr0.0077438
X-RAY DIFFRACTIONf_dihedral_angle_d16.3168937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.310.28981270.28082391X-RAY DIFFRACTION92.81
2.31-2.480.25421320.24972574X-RAY DIFFRACTION98.98
2.48-2.730.30861290.25342597X-RAY DIFFRACTION99.2
2.73-3.130.23421330.22172608X-RAY DIFFRACTION99.6
3.13-3.940.21071410.17722595X-RAY DIFFRACTION99.24
3.94-37.410.17231530.17062673X-RAY DIFFRACTION99.37
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1130770291-0.5878358403970.1369505460050.7359772657820.1995547027822.148221220170.244030276560.581258702429-0.07421344475760.101283545546-0.1329185154480.101638125321-0.291005386827-0.268173278296-0.04860048982950.08025396196380.1007933151780.02222156704060.3059682071930.04298361269960.142652804426-31.512026378212.493437728515.1657887319
22.959351088640.174422138853-0.1635272139071.03032609463-0.3009789543422.597862844450.1014138327510.291946717176-0.00220783324921-0.0716710966306-0.0343671696162-0.045177410695-0.02062368542640.16429210735-0.02776674254010.09097599272370.02501747606960.01018524355630.112001428050.004631443755470.0947009851828-17.65782429288.3234129754118.8544970039
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label seq-ID
11(chain 'B' and resid 7 through 67)BA7 - 672 - 55
22(chain 'A' and resid 68 through 328)AB - C68 - 328253

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