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- PDB-2buz: Crystal Structure of Protocatechuate 3,4-Dioxygenase from Acineto... -

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Basic information

Entry
Database: PDB / ID: 2buz
TitleCrystal Structure of Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 Mutant R133H in Complex with 4-Nitrocatechol
Components
  • PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
  • PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
KeywordsOXIDOREDUCTASE / DIOXYGENASE / AROMATIC DEGRADATION / NON-HEME IRON / BETA- SANDWICH / MIXED ALPHA/BETA STRUCTURE OXIDOREDUCTASE
Function / homology
Function and homology information


protocatechuate 3,4-dioxygenase / protocatechuate 3,4-dioxygenase activity / 3,4-dihydroxybenzoate catabolic process / beta-ketoadipate pathway / ferric iron binding
Similarity search - Function
Protocatechuate 3,4-dioxygenase, beta subunit / Protocatechuate 3,4-dioxygenase, alpha subunit / Protocatechuate 3,4-dioxygenase beta subunit, N-terminal / Protocatechuate 3,4-dioxygenase beta subunit N terminal / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenases signature. / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core ...Protocatechuate 3,4-dioxygenase, beta subunit / Protocatechuate 3,4-dioxygenase, alpha subunit / Protocatechuate 3,4-dioxygenase beta subunit, N-terminal / Protocatechuate 3,4-dioxygenase beta subunit N terminal / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenases signature. / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Sandwich / Mainly Beta
Similarity search - Domain/homology
4-NITROCATECHOL / : / Protocatechuate 3,4-dioxygenase alpha chain / Protocatechuate 3,4-dioxygenase beta chain
Similarity search - Component
Biological speciesACINETOBACTER CALCOACETICUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVetting, M.W. / Valley, M.P. / D'Argenio, D.A. / Ornston, L.N. / Lipscomb, J.D. / Ohlendorf, D.H.
CitationJournal: Ph D Thesis / Year: 2001
Title: Crystallographic Studies of Intradiol Dioxygenases
Authors: Vetting, M.W.
History
DepositionJun 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
B: PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2834
Polymers51,0722
Non-polymers2112
Water3,981221
1
A: PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
B: PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)615,39648
Polymers612,86524
Non-polymers2,53124
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)145.090, 145.090, 145.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-2054-

HOH

DetailsTHE PHYSIOLOGICAL STATE OF THE MOLECULE IS A (AB)12DODECAMER.FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

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Components

#1: Protein PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN / PROTOCATECHUATE 3 / 4-DIOXYGENASE / 3 / 4-PCD


Mass: 23489.053 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER CALCOACETICUS (bacteria) / Strain: ADP1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B86DE3
References: UniProt: P20371, protocatechuate 3,4-dioxygenase
#2: Protein PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN / PROTOCATECHUATE 3 / 4-DIOXYGENASE / 3 / 4-PCD


Mass: 27583.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER CALCOACETICUS (bacteria) / Strain: ADP1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B86DE3
References: UniProt: P20372, protocatechuate 3,4-dioxygenase
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-4NC / 4-NITROCATECHOL


Mass: 155.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE ARG 142 HIS, CHAIN A
Sequence detailsRESIDUES ARE NUMBERED TO CORRELATE WITH RESIDUE NUMBERING OF 3,4-PCD FROM PSEUDOMONAS PUTIDA ...RESIDUES ARE NUMBERED TO CORRELATE WITH RESIDUE NUMBERING OF 3,4-PCD FROM PSEUDOMONAS PUTIDA STRUCTURE, AND SO DO NOT EXACTLY CORRELATE WITH WHAT ONE WOULD EXPECT FOR A SEQUENTIAL NUMBERING. THIS INCLUDES AN INSERTION OF 5 RESIDUES IN THE A SUBUNIT BETWEEN K88 AND F89.

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Description: CRYSTAL WAS SOAKED IN 2.0 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5, 30-MM-4-NITROCATECHOL WITHIN AN AEROBIC ENVIRONMENT PRIOR TO DATA COLLECTION.
Crystal growpH: 8.5
Details: 1.8 M AMMONIUM SULFATE, 100 MM TRIS-MALEATE PH 7.5, 0.08% PEG4000 PROTEIN AT 20 MG/ML

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: OSMIC CONFOCAL MAXFLUX OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 46410 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1refinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EO2

1eo2


Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2356 5 %RANDOM
Rwork0.173 ---
obs0.173 46410 99.4 %-
Displacement parametersBiso mean: 29.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 12 221 3760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
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_deg2.02
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 1.8→1.86 Å /
Rfactor% reflection
Rfree0.314 5 %
Rwork0.278 -

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