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- PDB-1eoc: CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-D... -

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Basic information

Entry
Database: PDB / ID: 1eoc
TitleCRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 4-NITROCATECHOL
Components
  • PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
  • PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
KeywordsOXIDOREDUCTASE / beta-sandwich / mixed alpha/beta structure / dioxygenase / biodegradation
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 / Intradiol ring-cleavage dioxygenases signature. / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase ...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 / Intradiol ring-cleavage dioxygenases signature. / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / 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 sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsVetting, M.W. / D'Argenio, D.A. / Ornston, L.N. / Ohlendorf, D.H.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase.
Authors: Vetting, M.W. / D'Argenio, D.A. / Ornston, L.N. / Ohlendorf, D.H.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-ray Analysis of Protocatechuate 3,4-dioxygenase from Acinetobacter calcoaceticus
Authors: Vetting, M.W. / Earhart, C.A. / Ohlendorf, D.H.
#2: Journal: J.Bacteriol. / Year: 1999
Title: Substitution, Insertion, Deletion, Suppression, and Altered Substrate Specificity in Functional Protocatechuate 3,4-dioxygenases.
Authors: D'Argenio, D.A. / Vetting, M.W. / Ohlendorf, D.H. / Ornston, L.N.
#3: Journal: Biochemistry / Year: 1997
Title: Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-dioxygenase: Endogenous Fe3+ Ligand Displacement in Response to Substrate binding.
Authors: Orville, A.M. / Lipscomb, J.D. / Ohlendorf, D.H.
#4: Journal: J.Mol.Biol. / Year: 1994
Title: Structure of Protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15 A resolution
Authors: Ohlendorf, D.H. / Orville, A.M. / Lipscomb, J.D.
History
DepositionMar 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
B: PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3024
Polymers51,0912
Non-polymers2112
Water3,351186
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)615,62548
Polymers613,09424
Non-polymers2,53124
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area149600 Å2
ΔGint-645 kcal/mol
Surface area171120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.300, 144.300, 144.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsThe biological assembly is a dodecamer (AB) X 12 constructed from the 23(T) symmetry of the space group acting on the A and B subunits in the assymetric unit.

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Components

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


Mass: 23508.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Production host: Escherichia coli (E. coli)
References: UniProt: P20371, protocatechuate 3,4-dioxygenase
#2: Protein PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris-HCl pH 7.0, 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Crystal was soaked in 30mM 4-nitrocatechol at pH 8.5
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.8 Mammonium sulfate1reservoir
350 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 113962 / Num. obs: 23742 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 100 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.5
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.332 / % possible all: 33.2
Reflection
*PLUS
Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 91.1 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1

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Processing

Software
NameClassification
CNSrefinement
X-GENdata scaling
CNSphasing
RefinementResolution: 2.25→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 972 -5% of reflections
Rwork0.171 ---
all0.171 23841 --
obs0.171 20128 84.4 %-
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 12 186 3726
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_bond_d0.0059
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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