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- PDB-2cmh: Crystal Structure of Spermidine Synthase from Helicobacter Pylori -

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Basic information

Entry
Database: PDB / ID: 2cmh
TitleCrystal Structure of Spermidine Synthase from Helicobacter Pylori
ComponentsSPERMIDINE SYNTHASE
KeywordsTRANSFERASE / PUTRESCINE AMINOPROPYLTRANSFERASE / SPERMIDINE BIOSYNTHESIS / SPEE / SPERMIDINE SYNTHASE / HELICOBACTER PYLORI / POLYAMINE BIOSYNTHESIS
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / polyamine biosynthetic process / spermidine biosynthetic process / cytosol
Similarity search - Function
Spermidine synthase, tetramerisation domain / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain / Spermidine Synthase; Chain: A, domain 2 / Vaccinia Virus protein VP39 ...Spermidine synthase, tetramerisation domain / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain / Spermidine Synthase; Chain: A, domain 2 / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSun, Y.-J. / Lu, P.-K.
CitationJournal: Proteins: Struct., Funct., Bioinf. / Year: 2007
Title: Crystal Structure of Helicobacter Pylori Spermidine Synthase: A Rossmann-Like Fold with a Distinct Active Site
Authors: Lu, P.-K. / Tsai, J.-Y. / Chien, H.Y. / Huang, H. / Chu, C.-H. / Sun, Y.-J.
History
DepositionMay 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPERMIDINE SYNTHASE
B: SPERMIDINE SYNTHASE
C: SPERMIDINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)91,7573
Polymers91,7573
Non-polymers00
Water8,305461
1
B: SPERMIDINE SYNTHASE
C: SPERMIDINE SYNTHASE

B: SPERMIDINE SYNTHASE
C: SPERMIDINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)122,3424
Polymers122,3424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9030 Å2
ΔGint-64.9 kcal/mol
Surface area42970 Å2
MethodPISA
2
A: SPERMIDINE SYNTHASE

A: SPERMIDINE SYNTHASE
B: SPERMIDINE SYNTHASE
C: SPERMIDINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)122,3424
Polymers122,3424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_565x,-y+1,-z1
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.526, 126.468, 143.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2023-

HOH

21C-2107-

HOH

31C-2121-

HOH

DetailsTHIS PROTEIN WAS DETECTED AS DIMER/TETRAMER WITH SIZE-EXCLUSION CHROMATOGRAPHY. THE TETRAMERIC STATES WERE OBSERVED IN 2CMH AS TYPE I TETRAMER (BCB'C'/BIOMOLECULE 1) AND TYPE II TETRAMER (BCAA'/BIOMOLECULE 2).

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Components

#1: Protein SPERMIDINE SYNTHASE / PUTRESCINE AMINOPROPYLTRANSFERASE / SPDSY


Mass: 30585.615 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: O25503, spermidine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.42 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 40302 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.9 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 45.89
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 15 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 10.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 20549.92 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1932 5 %RANDOM
Rwork0.221 ---
obs0.221 38619 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.6019 Å2 / ksol: 0.440619 e/Å3
Displacement parametersBiso mean: 10 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2--0.51 Å20 Å2
3----3.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.3→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 0 461 6913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 292 4.9 %
Rwork0.219 5717 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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