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- PDB-2dvu: Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexe... -

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Basic information

Entry
Database: PDB / ID: 2dvu
TitleCrystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with 2,6-Dihydroxybenzoate
ComponentsThermophilic reversible gamma-resorcylate decarboxylase
KeywordsLYASE / TIM BARREL
Function / homology
Function and homology information


gamma-resorcylate decarboxylase / organic substance metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2,6-DIHYDROXYBENZOIC ACID / Gamma-resorcylate decarboxylase
Similarity search - Component
Biological speciesRhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGoto, M.
CitationJournal: To be Published
Title: Crystal Structures of Nonoxidative Zn-Dependent 2,6-Dihydroxybenzoate (gamma-Resorcylate) Decarboxylase from Rhizobium sp. Strain MTP-10005
Authors: Goto, M. / Hayashi, H. / Miyahara, I. / Hirotsu, K. / Yoshida, M. / Oikawa, T.
History
DepositionAug 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Thermophilic reversible gamma-resorcylate decarboxylase
B: Thermophilic reversible gamma-resorcylate decarboxylase
C: Thermophilic reversible gamma-resorcylate decarboxylase
D: Thermophilic reversible gamma-resorcylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,75212
Polymers149,8744
Non-polymers8788
Water18,6281034
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18500 Å2
ΔGint-234 kcal/mol
Surface area40900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.071, 113.611, 119.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer same as the asymmetric unit of a crystal structure.

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Components

#1: Protein
Thermophilic reversible gamma-resorcylate decarboxylase / 2 / 6-Dihydroxybenzoate Decarboxylase


Mass: 37468.430 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rhizobium sp. (bacteria) / Strain: MTP-10005
References: UniProt: Q60GU1, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GRE / 2,6-DIHYDROXYBENZOIC ACID / 2,6-Dihydroxybenzoic acid


Mass: 154.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1034 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, HEPES-Na, Ethyleneglycol, 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40.226 Å / Num. all: 116818 / Num. obs: 116804 / % possible obs: 100 % / Biso Wilson estimate: 14.2 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVT

2dvt


Resolution: 1.9→40.22 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3168539.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 11691 10 %RANDOM
Rwork0.176 ---
obs0.176 116804 99.8 %-
all-116818 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.911 Å2 / ksol: 0.326022 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---0.54 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10460 0 48 1034 11542
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.462
X-RAY DIFFRACTIONc_scbond_it17.12
X-RAY DIFFRACTIONc_scangle_it11.622.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 1967 10.2 %
Rwork0.193 17293 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramCNS_LOCAL:top.wat
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gre.paramgre.top

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