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- PDB-3iwc: T. maritima AdoMetDC complex with S-Adenosylmethionine methyl ester -

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Basic information

Entry
Database: PDB / ID: 3iwc
TitleT. maritima AdoMetDC complex with S-Adenosylmethionine methyl ester
Components(S-adenosylmethionine decarboxylase) x 2
KeywordsLYASE / Autocatalytic cleavage / Decarboxylase / Polyamine biosynthesis / Pyruvate / S-adenosyl-L-methionine / Schiff base / Spermidine biosynthesis / Zymogen
Function / homology
Function and homology information


adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol
Similarity search - Function
Double Stranded RNA Binding Domain - #750 / S-adenosylmethionine decarboxylase domain / S-adenosylmethionine decarboxylase, N-terminal / S-adenosylmethionine decarboxylase, C-terminal / S-adenosylmethionine decarboxylase family, prokaryotic / S-adenosylmethionine decarboxylase proenzyme / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 / Double Stranded RNA Binding Domain ...Double Stranded RNA Binding Domain - #750 / S-adenosylmethionine decarboxylase domain / S-adenosylmethionine decarboxylase, N-terminal / S-adenosylmethionine decarboxylase, C-terminal / S-adenosylmethionine decarboxylase family, prokaryotic / S-adenosylmethionine decarboxylase proenzyme / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE METHYL ESTER / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBale, S. / Kavita, B. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Complexes of Thermotoga maritimaS-adenosylmethionine decarboxylase provide insights into substrate specificity.
Authors: Bale, S. / Baba, K. / McCloskey, D.E. / Pegg, A.E. / Ealick, S.E.
History
DepositionSep 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: S-adenosylmethionine decarboxylase
A: S-adenosylmethionine decarboxylase
D: S-adenosylmethionine decarboxylase
C: S-adenosylmethionine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4446
Polymers29,6154
Non-polymers8292
Water1,946108
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14010 Å2
ΔGint-62 kcal/mol
Surface area9920 Å2
MethodPISA
2
B: S-adenosylmethionine decarboxylase
A: S-adenosylmethionine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2223
Polymers14,8082
Non-polymers4141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-21 kcal/mol
Surface area7250 Å2
MethodPISA
3
D: S-adenosylmethionine decarboxylase
C: S-adenosylmethionine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2223
Polymers14,8082
Non-polymers4141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-22 kcal/mol
Surface area7220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.204, 105.204, 70.062
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Detailsbiological assembly is a dimer in the asymmetric unit

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Components

#1: Protein S-adenosylmethionine decarboxylase / AdoMetDC / SAMDC / S-adenosylmethionine decarboxylase beta chain / S-adenosylmethionine ...AdoMetDC / SAMDC / S-adenosylmethionine decarboxylase beta chain / S-adenosylmethionine decarboxylase alpha chain


Mass: 6999.928 Da / Num. of mol.: 2 / Fragment: residues 1-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: speH, TM_0655 / Plasmid: pTmSpeD.28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q9WZC3, adenosylmethionine decarboxylase
#2: Protein S-adenosylmethionine decarboxylase / AdoMetDC / SAMDC / S-adenosylmethionine decarboxylase beta chain / S-adenosylmethionine ...AdoMetDC / SAMDC / S-adenosylmethionine decarboxylase beta chain / S-adenosylmethionine decarboxylase alpha chain


Mass: 7807.784 Da / Num. of mol.: 2 / Fragment: residues 64-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: speH, TM_0655 / Plasmid: pTmSpeD.28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q9WZC3, adenosylmethionine decarboxylase
#3: Chemical ChemComp-SMM / S-ADENOSYLMETHIONINE METHYL ESTER


Mass: 414.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.8 M ammonium formate, 100 mM HEPES, pH 8.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 22459 / Num. obs: 22259 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Χ2: 1.317 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2067 / Rsym value: 0.216 / Χ2: 0.544 / % possible all: 90.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TLU

1tlu


Resolution: 1.9→32.7 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 86489 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2207 9.9 %RANDOM
Rwork0.212 ---
all0.212 22459 --
obs0.212 22259 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.519 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 80.4 Å2 / Biso mean: 32.829 Å2 / Biso min: 14.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 56 108 2081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.031
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 331 9.8 %
Rwork0.25 3038 -
all-3369 -
obs-2067 88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2&_1_PARAMETER_INFILE_2all.top
X-RAY DIFFRACTION3&_1_PARAMETER_INFILE_3&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4water_rep.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5all.param

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