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- PDB-9p7q: 273K human S-adenosylmethionine decarboxylase -

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Basic information

Entry
Database: PDB / ID: 9p7q
Title273K human S-adenosylmethionine decarboxylase
Components(S-adenosylmethionine decarboxylase ...) x 2
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: 2.21 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 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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)40,3075
Polymers40,0612
Non-polymers2463
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-38 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.978, 45.018, 72.061
Angle α, β, γ (deg.)90.000, 105.109, 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
Components on special symmetry positions
IDModelComponents
11A-403-

CL

21A-586-

HOH

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Components

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S-adenosylmethionine decarboxylase ... , 2 types, 2 molecules BA

#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 (E. coli) / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P17707

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Non-polymers , 4 types, 114 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


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


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 35.11 %
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: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 X 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: 2.21→34.86 Å / Num. obs: 14760 / % possible obs: 97.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 11.01 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.286 / Rpim(I) all: 0.192 / Rrim(I) all: 0.347 / Net I/σ(I): 4.5
Reflection shellResolution: 2.21→2.27 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1089 / CC1/2: 0.34 / Rpim(I) all: 1.22 / Rrim(I) all: 2.246 / Χ2: 0.87 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
STARANISOdata scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→34.86 Å / SU ML: 0.2543 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2588 791 5.36 %
Rwork0.2197 13970 -
obs0.2219 14760 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.41 Å2
Refinement stepCycle: LAST / Resolution: 2.21→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 15 111 2612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842568
X-RAY DIFFRACTIONf_angle_d1.09823464
X-RAY DIFFRACTIONf_chiral_restr0.0585373
X-RAY DIFFRACTIONf_plane_restr0.0193442
X-RAY DIFFRACTIONf_dihedral_angle_d15.7417946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.340.311300.27842215X-RAY DIFFRACTION92.69
2.34-2.520.28551280.2632231X-RAY DIFFRACTION92.98
2.52-2.780.31571550.26692354X-RAY DIFFRACTION98.66
2.78-3.180.31081290.24892379X-RAY DIFFRACTION98.16
3.18-4.010.22341190.19712352X-RAY DIFFRACTION95.89
4.01-34.860.21821300.18182439X-RAY DIFFRACTION97.53
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)
13.817893409250.3181778430121.179708446985.57027152171-0.6371600736935.0411632320.216871631807-0.285409262003-0.4124760766920.0832797132701-0.06176360976010.06568524795110.0731278755487-0.124566019679-0.139372857890.1435917137710.02829251093660.01949054605760.12891091137-0.07976174405490.113952447223-30.47410.13620.489
28.23202418955-0.7505797244210.7842563544542.193926258242.26457639936.850715911910.2065478286580.408783516910.515987882904-0.37614252533-0.06416671895380.227443475856-0.836384268271-0.0734343609275-0.1776352647090.300819337480.1308462249510.1199068423780.3488372665120.1233083303480.287278232187-35.09219.83913.953
34.38822890757-1.8130672787-2.078350570546.372779127893.977519438859.17128041065-0.3672771962060.591015285577-0.0580537047654-0.3444400102890.939435267881-0.141953103958-1.027000190140.390265093669-0.6021103493430.2733110919910.0724738826660.0410520833830.4797196559050.02442125577010.188966459394-29.78414.9258.104
44.250292108110.134435893522-3.462286181265.66706371685-6.43023822872.081988169260.09099355856190.223175351804-0.1939075901260.667363330745-0.221989442302-0.236947722605-0.112032841276-0.1596480982960.1888385590670.2804888388750.0292194449146-0.04519210726240.36533132283-0.006043664501140.168679223029-30.2858.28210.59
54.012800665190.1631085946371.626105207981.411081986230.4669399311473.299549750710.0558548188926-0.1626090327430.4886163168190.03076566103770.01666525106210.00738860834604-0.2733200895510.0640649301567-0.07424085388380.2157039180130.02036083682670.06600791781890.173145700218-0.01536455689130.209887388827-23.24615.55125.972
61.84470320586-0.201672540912.331939943653.631140701650.02829580318783.330835351550.229302155910.0172625429992-0.3077155108280.439945966146-0.2439040502560.02363019426940.178539026301-0.0199540656004-0.005615153230130.182009159167-0.0018826127296-0.05244437649670.171515435252-0.04007886647120.222335394983-16.6134.9519.322
73.865072910291.31804950401-0.3136714686922.0531073092-0.2705260839044.100765867570.004089076250230.610306945758-0.250605781511-0.2961580960840.0693037387379-0.1161167485410.2921344293820.264744743177-0.05747802314240.1672233118840.0457792217747-0.01001098827830.301818125936-0.05318410129610.191236978447-15.2574.5578.558
85.13943674454-1.58078683084-0.4925213783474.158684920990.02969830094445.84898366539-0.0525347454369-0.292747039987-0.1836633741960.2664376803970.0443320459826-0.06408396860150.6511424007040.2237579752840.05830111977820.301472270687-0.00564931550554-0.05506882272830.211162380830.04509461001280.165105365588-8.450.67526.151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 6:36 )B6 - 36
2X-RAY DIFFRACTION2( CHAIN B AND RESID 37:47 )B37 - 47
3X-RAY DIFFRACTION3( CHAIN B AND RESID 48:56 )B48 - 56
4X-RAY DIFFRACTION4( CHAIN B AND RESID 57:67 )B57 - 67
5X-RAY DIFFRACTION5( CHAIN A AND RESID 69:162 )A69 - 162
6X-RAY DIFFRACTION6( CHAIN A AND RESID 163:192 )A163 - 192
7X-RAY DIFFRACTION7( CHAIN A AND RESID 193:287 )A193 - 287
8X-RAY DIFFRACTION8( CHAIN A AND RESID 288:328 )A288 - 328

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