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- PDB-1vr7: Crystal structure of S-adenosylmethionine decarboxylase proenzyme... -

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Basic information

Entry
Database: PDB / ID: 1vr7
TitleCrystal structure of S-adenosylmethionine decarboxylase proenzyme (TM0655) from THERMOTOGA MARITIMA at 1.2 A resolution
ComponentsS-adenosylmethionine decarboxylase proenzyme
KeywordsLYASE / TM0655 / S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol
Similarity search - Function
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 / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of S-adenosylmethionine decarboxylase proenzyme (TM0655) from Thermotoga Maritima at 1.2 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine decarboxylase proenzyme
B: S-adenosylmethionine decarboxylase proenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8803
Polymers32,8182
Non-polymers621
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-21 kcal/mol
Surface area10640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.298, 105.298, 69.427
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein S-adenosylmethionine decarboxylase proenzyme / AdoMetDC / SamDC


Mass: 16409.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0655 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZC3, adenosylmethionine decarboxylase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 277 K / pH: 8
Details: 1.0M LiCl, 10.0% PEG-6000, 0.1M TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979594
DetectorType: ADSC / Detector: CCD / Date: Jan 5, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979594 Å / Relative weight: 1
ReflectionResolution: 1.2→55.24 Å / Num. obs: 88939 / % possible obs: 99 % / Redundancy: 3 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.2-1.2393.51.90.5751.262370.575
1.23-1.2696.82.30.4971.262640.497
1.26-1.398.52.50.3911.862090.391
1.3-1.3499.72.60.3352.260820.335
1.34-1.3999.82.60.2492.859630.249
1.39-1.4399.62.60.1923.856390.192
1.43-1.4999.72.70.1542.955150.154
1.49-1.5599.72.70.1274.353260.127
1.55-1.6299.72.70.1115.750870.111
1.62-1.799.92.70.1016.348840.101
1.7-1.7999.92.70.0936.646200.093
1.79-1.999.92.70.0886.343790.088
1.9-2.031002.90.0876.941510.087
2.03-2.191003.40.0778.338200.077
2.19-2.41004.10.0679.735410.067
2.4-2.681005.20.0679.231830.067
2.68-3.11005.50.05511.328290.055
3.1-3.791005.50.04612.923760.046
3.79-5.371005.10.04213.418230.042
5.37-55.2499.94.80.04212.810110.042

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
SCALAdata scaling
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
SHELXL-97refinement
RefinementResolution: 1.2→55 Å / Num. parameters: 19113 / Num. restraintsaints: 24162 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: 1. THE CRYSTAL WAS TWINNED ACCORDING TO THE TWIN LAW 1 0 0 -1 -1 0 0 0 -1. THE TWINNING FRACTION WAS REFINED IN SHELXL AND WAS 0.31 IN THE FINAL CYCLE. 2. THE FINAL REFINEMENT CYCLE WAS ...Details: 1. THE CRYSTAL WAS TWINNED ACCORDING TO THE TWIN LAW 1 0 0 -1 -1 0 0 0 -1. THE TWINNING FRACTION WAS REFINED IN SHELXL AND WAS 0.31 IN THE FINAL CYCLE. 2. THE FINAL REFINEMENT CYCLE WAS AGAINST ALL DATA. THE FREE R VALUES ABOVE ARE FROM THE PREVIOUS CYCLE. 3. THE TWIN LAW WAS USED IN SELECTING THE REFLECTIONS FOR THE TEST SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.15 4307 4.8 %RANDOM
all0.12 88936 --
obs--99 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 22.152 Å2
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 1716 / Occupancy sum non hydrogen: 2083
Refinement stepCycle: LAST / Resolution: 1.2→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 4 153 2081
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.0350
X-RAY DIFFRACTIONs_similar_dist00
X-RAY DIFFRACTIONs_from_restr_planes0.030
X-RAY DIFFRACTIONs_zero_chiral_vol0.0810
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.080
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0490
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0050
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0620
X-RAY DIFFRACTIONs_approx_iso_adps0.090

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