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- PDB-3pcb: STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYD... -

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Entry
Database: PDB / ID: 3pcb
TitleSTRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYBENZOATE
Components
  • Protocatechuate 3,4-dioxygenase alpha chain
  • Protocatechuate 3,4-dioxygenase beta chain
KeywordsDIOXYGENASE / IRON / NONHEME / METALLOPROTEIN / 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
3-HYDROXYBENZOIC ACID / : / Protocatechuate 3,4-dioxygenase alpha chain / Protocatechuate 3,4-dioxygenase beta chain
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / NATIVE MODEL PHASES / Resolution: 2.19 Å
AuthorsElango, N. / Orville, A.M. / Lipscomb, J.D. / Ohlendorf, D.H.
Citation
Journal: Biochemistry / Year: 1997
Title: Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site.
Authors: Orville, A.M. / Elango, N. / Lipscomb, J.D. / Ohlendorf, D.H.
#1: 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.
#2: Journal: Nature / Year: 1988
Title: Structure and Assembly of Protocatechuate 3,4-Dioxygenase
Authors: Ohlendorf, D.H. / Lipscomb, J.D. / Weber, P.C.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Determination of the Quaternary Structure of Protocatechuate 3,4-Dioxygenase from Pseudomonas Aeruginosa
Authors: Ohlendorf, D.H. / Weber, P.C. / Lipscomb, J.D.
History
DepositionApr 25, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.dist / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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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
M: Protocatechuate 3,4-dioxygenase beta chain
B: Protocatechuate 3,4-dioxygenase alpha chain
N: Protocatechuate 3,4-dioxygenase beta chain
C: Protocatechuate 3,4-dioxygenase alpha chain
O: Protocatechuate 3,4-dioxygenase beta chain
D: Protocatechuate 3,4-dioxygenase alpha chain
P: Protocatechuate 3,4-dioxygenase beta chain
E: Protocatechuate 3,4-dioxygenase alpha chain
Q: Protocatechuate 3,4-dioxygenase beta chain
F: Protocatechuate 3,4-dioxygenase alpha chain
R: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,30030
Polymers294,30712
Non-polymers1,99318
Water25,5091416
1
A: Protocatechuate 3,4-dioxygenase alpha chain
M: Protocatechuate 3,4-dioxygenase beta chain
B: Protocatechuate 3,4-dioxygenase alpha chain
N: Protocatechuate 3,4-dioxygenase beta chain
C: Protocatechuate 3,4-dioxygenase alpha chain
O: Protocatechuate 3,4-dioxygenase beta chain
D: Protocatechuate 3,4-dioxygenase alpha chain
P: Protocatechuate 3,4-dioxygenase beta chain
E: Protocatechuate 3,4-dioxygenase alpha chain
Q: Protocatechuate 3,4-dioxygenase beta chain
F: Protocatechuate 3,4-dioxygenase alpha chain
R: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

A: Protocatechuate 3,4-dioxygenase alpha chain
M: Protocatechuate 3,4-dioxygenase beta chain
B: Protocatechuate 3,4-dioxygenase alpha chain
N: Protocatechuate 3,4-dioxygenase beta chain
C: Protocatechuate 3,4-dioxygenase alpha chain
O: Protocatechuate 3,4-dioxygenase beta chain
D: Protocatechuate 3,4-dioxygenase alpha chain
P: Protocatechuate 3,4-dioxygenase beta chain
E: Protocatechuate 3,4-dioxygenase alpha chain
Q: Protocatechuate 3,4-dioxygenase beta chain
F: Protocatechuate 3,4-dioxygenase alpha chain
R: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)592,60060
Polymers588,61524
Non-polymers3,98536
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area143800 Å2
ΔGint-745 kcal/mol
Surface area163330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)196.950, 127.560, 134.310
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(0.22413831, 0.97412111, -0.05310336), (0.23006211, 0.97305075), (0.94604151, -0.23031518, -0.22413831)
2given(0.22410836, 0.23056837, 0.94786928), (0.97211214, -0.23031502), (-0.0529868, 0.97318146, -0.22410836)
3given(-0.89390991, 0.44870945), (-1), (0.44778436, 0.8939099)
4given(0.22413831, -0.97412111, -0.05310336), (-0.23006211, -0.97305075), (0.94604151, 0.23031518, -0.22413831)
5given(-0.22410836, 0.23056837, -0.94786928), (-0.97211214, 0.23031502), (0.0529868, 0.97318146, 0.22410836)
DetailsTHE ACTIVE FORM OF THE ENZYME IS THE WHOLE UNIT CELL CONTENT. IT CONSISTS OF 12 PROTOMERS. EACH PROTOMER IS MADE OF TWO POLYPEPTIDE CHAINS AND ONE FE(III). THE ASYMMETRIC UNIT CONSISTS OF 6 PROTOMERS. THEY ARE: CHAINS (A, M), CHAINS (B, N), CHAINS (C, O), CHAINS (D, P), CHAINS (E, Q), CHAINS (F, R). EACH PROTOMER CONTAINS AN ACTIVE SITE WITH FE(III) AS THE CENTER AND A VESTIGIAL SITE. THE ACTIVE SITES ARE NAMED: ACA, ACB, ACC, ACD, ACE, ACF. THE VESTIGIAL SITES ARE NAMED VEA, VEB, VEC, VED, VEE AND VEF. THE CHAIN IDENTIFIERS HAVE BEEN ASSIGNED AS FOLLOWS: ALPHA BETA WATERS A M G B N H C O I D P J E Q K F R L

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Components

#1: Protein
Protocatechuate 3,4-dioxygenase alpha chain / 3 / 4-PCD


Mass: 22278.812 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: ENTRY CONTAINS ALPHA/BETA 6-MER / Source: (natural) Pseudomonas putida (bacteria)
References: UniProt: P00436, protocatechuate 3,4-dioxygenase
#2: Protein
Protocatechuate 3,4-dioxygenase beta chain / 3 / 4-PCD


Mass: 26772.404 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: ENTRY CONTAINS ALPHA/BETA 6-MER / Source: (natural) Pseudomonas putida (bacteria)
References: UniProt: P00437, protocatechuate 3,4-dioxygenase
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-3HB / 3-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1416 / 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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growpH: 8.4 / Details: pH 8.4
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: interface diffusion
Details: or hanging drop vapor diffusion, Ohlendorf, D.H., (1994) J.Mol.Biol., 244, 586.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-75 mg/mlprotein1drop
21.5-1.8 Mammonium sulfate1reservoir
350 mMTris-HCl1reservoir
410 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 3, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→15 Å / Num. obs: 132191 / % possible obs: 78.2 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rsym value: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 2.19→2.28 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / % possible all: 36.5
Reflection
*PLUS
Num. measured all: 247730 / Rmerge(I) obs: 0.152
Reflection shell
*PLUS
% possible obs: 36.5 %

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Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: NATIVE MODEL PHASES / Resolution: 2.19→6 Å / σ(F): 1
Details: APART FROM BINDING THE INHIBITOR AT THE ACTIVE SITE OF EACH PROTOMER, ONE MOLECULE OF THE INHIBITOR CORRESPONDING TO EACH PROTOMER ALSO BINDS AT THE LOCAL THREE-FOLD SYMMETRY. THE ...Details: APART FROM BINDING THE INHIBITOR AT THE ACTIVE SITE OF EACH PROTOMER, ONE MOLECULE OF THE INHIBITOR CORRESPONDING TO EACH PROTOMER ALSO BINDS AT THE LOCAL THREE-FOLD SYMMETRY. THE NONSTANDARD UNIT CELL I 2 WAS CHOSEN OVER THE EQUIVALENT C 2 CELL BECAUSE OF THE CONVENIENCE OF HAVING A BETA ANGLE NEAR 90 DEGREES AND TO MAINTAIN CONSISTENCY WITH THE INITIAL CRYSTALLIZATION REPORT. TO CONVERT FROM FRACTIONAL I 2 TO FRACTIONAL C 2, USE THE FOLLOWING TRANSFORMATION: [ 1.0 ][ 0.0 ][ 0.0 ] (XFRAC_I2) (XFRAC_C2) [ 0.0 ][ 1.0 ][ 0.0 ] X (YFRAC_I2) = (YFRAC_C2) [ -1.0 ][ 0.0 ][ 1.0 ] (ZFRAC_I2) (ZFRAC_C2) THE ORTHOGONAL COORDINATE SYSTEM CHOSEN FOR THIS ENTRY IS THAT DEFINED BY THE LOCAL SYMMETRY OF THE COMPLEX (23).
RfactorNum. reflection% reflection
Rwork0.159 --
obs-110643 78.2 %
Displacement parametersBiso mean: 25.76 Å2
Refinement stepCycle: LAST / Resolution: 2.19→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20466 0 150 1416 22032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.03
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.5051
X-RAY DIFFRACTIONp_mcangle_it0.9052
X-RAY DIFFRACTIONp_scbond_it0.9631.5
X-RAY DIFFRACTIONp_scangle_it1.613
X-RAY DIFFRACTIONp_plane_restr0.0120.03
X-RAY DIFFRACTIONp_chiral_restr0.220.3
X-RAY DIFFRACTIONp_singtor_nbd0.1770.5
X-RAY DIFFRACTIONp_multtor_nbd0.2040.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1720.5
X-RAY DIFFRACTIONp_planar_tor2.13
X-RAY DIFFRACTIONp_staggered_tor17.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.4 Å / Rfactor Rwork: 0.211

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