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

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Basic information

Entry
Database: PDB / ID: 3pce
TitleSTRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE
Components(PROTOCATECHUATE 3,4- ...) x 2
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-HYDROXYPHENYLACETATE / BETA-MERCAPTOETHANOL / : / 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: 2.06 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 29, 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_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.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 / _pdbx_validate_close_contact.dist / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTOCATECHUATE 3,4-DIOXYGENASE
M: PROTOCATECHUATE 3,4-DIOXYGENASE
B: PROTOCATECHUATE 3,4-DIOXYGENASE
N: PROTOCATECHUATE 3,4-DIOXYGENASE
C: PROTOCATECHUATE 3,4-DIOXYGENASE
O: PROTOCATECHUATE 3,4-DIOXYGENASE
D: PROTOCATECHUATE 3,4-DIOXYGENASE
P: PROTOCATECHUATE 3,4-DIOXYGENASE
E: PROTOCATECHUATE 3,4-DIOXYGENASE
Q: PROTOCATECHUATE 3,4-DIOXYGENASE
F: PROTOCATECHUATE 3,4-DIOXYGENASE
R: PROTOCATECHUATE 3,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,56730
Polymers293,85112
Non-polymers1,71718
Water26,0501446
1
A: PROTOCATECHUATE 3,4-DIOXYGENASE
M: PROTOCATECHUATE 3,4-DIOXYGENASE
B: PROTOCATECHUATE 3,4-DIOXYGENASE
N: PROTOCATECHUATE 3,4-DIOXYGENASE
C: PROTOCATECHUATE 3,4-DIOXYGENASE
O: PROTOCATECHUATE 3,4-DIOXYGENASE
D: PROTOCATECHUATE 3,4-DIOXYGENASE
P: PROTOCATECHUATE 3,4-DIOXYGENASE
E: PROTOCATECHUATE 3,4-DIOXYGENASE
Q: PROTOCATECHUATE 3,4-DIOXYGENASE
F: PROTOCATECHUATE 3,4-DIOXYGENASE
R: PROTOCATECHUATE 3,4-DIOXYGENASE
hetero molecules

A: PROTOCATECHUATE 3,4-DIOXYGENASE
M: PROTOCATECHUATE 3,4-DIOXYGENASE
B: PROTOCATECHUATE 3,4-DIOXYGENASE
N: PROTOCATECHUATE 3,4-DIOXYGENASE
C: PROTOCATECHUATE 3,4-DIOXYGENASE
O: PROTOCATECHUATE 3,4-DIOXYGENASE
D: PROTOCATECHUATE 3,4-DIOXYGENASE
P: PROTOCATECHUATE 3,4-DIOXYGENASE
E: PROTOCATECHUATE 3,4-DIOXYGENASE
Q: PROTOCATECHUATE 3,4-DIOXYGENASE
F: PROTOCATECHUATE 3,4-DIOXYGENASE
R: PROTOCATECHUATE 3,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)591,13560
Polymers587,70124
Non-polymers3,43336
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area144180 Å2
ΔGint-718 kcal/mol
Surface area163720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)196.570, 127.770, 134.630
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(0.22187355, 0.97438194, -0.05195037), (0.22791068, 0.97339621), (0.94759426, -0.22814148, -0.22187354)
2given(0.22207205, 0.22804161, 0.94845969), (0.97295202, -0.22781091), (-0.05199588, 0.9739373, -0.22207205)
3given(-0.89605376, 0.44394968), (-1), (0.44394143, 0.89605376)
4given(0.22187355, -0.97438194, -0.05195037), (-0.22791068, -0.97339621), (0.94759426, 0.22814148, -0.22187354)
5given(-0.22207205, 0.22804161, -0.94845969), (-0.97295202, 0.22781091), (0.05199588, 0.9739373, 0.22207205)
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

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PROTOCATECHUATE 3,4- ... , 2 types, 12 molecules ABCDEFMNOPQR

#1: Protein
PROTOCATECHUATE 3,4-DIOXYGENASE


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


Mass: 26696.287 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

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Non-polymers , 4 types, 1464 molecules

#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical
ChemComp-3HP / 3-HYDROXYPHENYLACETATE


Mass: 152.147 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1446 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsONE MOLECULE OF THE INHIBITOR 3-HYDROXY PHENYLACETATE AT THE ACTIVE SITE OF EACH PROTOMER.

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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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growpH: 8.4 / Details: pH 8.4
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: interface diffusion / Details: or hanging drop vapor diffusion
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: Mar 14, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→15 Å / Num. obs: 161694 / % possible obs: 79.8 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rsym value: 0.09 / Net I/σ(I): 10.1
Reflection shellResolution: 2.06→2.148 Å / Redundancy: 1.37 % / Mean I/σ(I) obs: 1.2 / % possible all: 37.8
Reflection
*PLUS
Num. measured all: 336503 / Rmerge(I) obs: 0.176
Reflection shell
*PLUS
% possible obs: 37.8 %

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Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: NATIVE MODEL PHASES / Resolution: 2.06→6 Å / σ(F): 1
Details: 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 ...Details: 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
Rwork0.169 --
obs-130591 79.8 %
Displacement parametersBiso mean: 24.18 Å2
Refinement stepCycle: LAST / Resolution: 2.06→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20466 0 96 1446 22008
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.03
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_it0.5431
X-RAY DIFFRACTIONp_mcangle_it0.9372
X-RAY DIFFRACTIONp_scbond_it1.0541.5
X-RAY DIFFRACTIONp_scangle_it1.7033
X-RAY DIFFRACTIONp_plane_restr0.0130.03
X-RAY DIFFRACTIONp_chiral_restr0.2220.3
X-RAY DIFFRACTIONp_singtor_nbd0.1760.5
X-RAY DIFFRACTIONp_multtor_nbd0.2040.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1490.5
X-RAY DIFFRACTIONp_planar_tor2.23
X-RAY DIFFRACTIONp_staggered_tor1715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rfactor obs: 0.227

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