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- PDB-2dgd: Crystal structure of ST0656, a function unknown protein from Sulf... -

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Basic information

Entry
Database: PDB / ID: 2dgd
TitleCrystal structure of ST0656, a function unknown protein from Sulfolobus tokodaii
Components223aa long hypothetical arylmalonate decarboxylase
KeywordsLYASE / OCTAMER / alpha/beta structure
Function / homology
Function and homology information


racemase and epimerase activity, acting on amino acids and derivatives
Similarity search - Function
Maleate isomerase/Arylmalonate decarboxylase / Arylmalonate decarboxylase / Rossmann fold - #1860 / Asp/Glu racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Arylmalonate decarboxylase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsTanaka, Y. / Sasaki, T. / Tanabe, E. / Yao, M. / Tanaka, I. / Kumagai, I. / Tsumoto, K.
CitationJournal: To be Published
Title: Crystal structure of ST0656, a function unknown protein from Sulfolobus tokodaii
Authors: Tanaka, Y. / Sasaki, T. / Tanabe, E. / Yao, M. / Tanaka, I. / Kumagai, I. / Tsumoto, K.
History
DepositionMar 10, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: 223aa long hypothetical arylmalonate decarboxylase
B: 223aa long hypothetical arylmalonate decarboxylase
C: 223aa long hypothetical arylmalonate decarboxylase
D: 223aa long hypothetical arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2686
Polymers103,0844
Non-polymers1842
Water3,963220
1
A: 223aa long hypothetical arylmalonate decarboxylase
B: 223aa long hypothetical arylmalonate decarboxylase
C: 223aa long hypothetical arylmalonate decarboxylase
D: 223aa long hypothetical arylmalonate decarboxylase
hetero molecules

A: 223aa long hypothetical arylmalonate decarboxylase
B: 223aa long hypothetical arylmalonate decarboxylase
C: 223aa long hypothetical arylmalonate decarboxylase
D: 223aa long hypothetical arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,53612
Polymers206,1688
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Unit cell
Length a, b, c (Å)131.221, 131.221, 125.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a octamer generated from the tetramer in the asymmetric unit by the operations: x-y+1, -y+2, -z+2/3.

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Components

#1: Protein
223aa long hypothetical arylmalonate decarboxylase


Mass: 25770.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: GenBank: 15621661, UniProt: Q974K3*PLUS, arylmalonate decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.6M NaCl, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792, 0.9795, 0.9685
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.96851
ReflectionResolution: 2.8→50 Å / Num. obs: 31282 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 78.4 Å2 / Rsym value: 0.094
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9 % / Num. unique all: 3052 / Rsym value: 0.429 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2110147.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2003 7.1 %RANDOM
Rwork0.188 ---
obs0.188 28075 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.3099 Å2 / ksol: 0.354468 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å24.79 Å20 Å2
2---2.37 Å20 Å2
3---4.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7144 0 12 220 7376
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 318 6.9 %
Rwork0.251 4293 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gol_xplor_2.paramgol_xplor_2.top

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