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- PDB-3gjy: Crystal structure of a probable spermidine synthase from Coryneba... -

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Basic information

Entry
Database: PDB / ID: 3gjy
TitleCrystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032
ComponentsSpermidine synthase
KeywordsTRANSFERASE / APC62791 / spermidine synthase / Corynebacterium glutamicum ATCC 13032 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyVaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Spermidine synthase
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsTan, K. / Li, H. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032.
Authors: Tan, K. / Li, H. / Freeman, L. / Joachimiak, A.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2622
Polymers35,2161
Non-polymers461
Water6,936385
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.909, 65.009, 87.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN.

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Components

#1: Protein Spermidine synthase


Mass: 35215.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 / Gene: Cgl1237, cg1394 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NR27
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Potassium sodium tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2008 / Details: Mirror
RadiationMonochromator: Si(111) crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.47→23 Å / Num. all: 51371 / Num. obs: 51371 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 43.5
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.88 / Num. unique all: 2418 / % possible all: 95.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→22.62 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.009 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.077 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19152 2614 5.1 %RANDOM
Rwork0.15704 ---
all0.1588 48639 --
obs0.1588 48639 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.47→22.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 0 388 2639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9453181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83423.274113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7415379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2041521
X-RAY DIFFRACTIONr_chiral_restr0.110.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211832
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4541.51445
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23122340
X-RAY DIFFRACTIONr_scbond_it3.143878
X-RAY DIFFRACTIONr_scangle_it4.5354.5821
X-RAY DIFFRACTIONr_rigid_bond_restr1.70232323
X-RAY DIFFRACTIONr_sphericity_free6.7583385
X-RAY DIFFRACTIONr_sphericity_bonded4.1532254
LS refinement shellResolution: 1.47→1.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 162 -
Rwork0.227 3414 -
obs-3576 95.72 %

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