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- PDB-2pcd: STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AER... -

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Entry
Database: PDB / ID: 2pcd
TitleSTRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTION
Components
  • PROTOCATECHUATE 3,4-DIOXYGENASE (ALPHA CHAIN)
  • PROTOCATECHUATE 3,4-DIOXYGENASE (BETA CHAIN)
KeywordsDIOXYGENASE
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
: / Protocatechuate 3,4-dioxygenase alpha chain / Protocatechuate 3,4-dioxygenase beta chain
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.15 Å
AuthorsOhlendorf, D.H. / Orville, A.M. / Lipscomb, J.D.
Citation
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.
#1: Journal: Nature / Year: 1988
Title: Structure and Assembly of Protocatechuate 3,4-Dioxygenase
Authors: Ohlendorf, D.H. / Lipscomb, J.D. / Weber, P.C.
#2: 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
DepositionJun 21, 1994Processing site: BNL
SupersessionDec 20, 1994ID: 1PCD
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 1.4Dec 11, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_biol
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[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 / _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_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _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
Remark 700SHEET SHEETS S1X AND S2X ARE HOMOLOGOUS EIGHT-STRANDED SHEETS WITH TOPOLOGY (-5, -1, 7, -5, 1, 1X, ...SHEET SHEETS S1X AND S2X ARE HOMOLOGOUS EIGHT-STRANDED SHEETS WITH TOPOLOGY (-5, -1, 7, -5, 1, 1X, 1). EACH SHEET IS FOLDED IN HALF WITH THE EDGES SEALED BY A 4 RESIDUE SEGMENT (37 - 40 OR 361 - 364) WHICH FORMS H-BONDS WITH EACH EDGE STRAND.

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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)294,18618
Polymers293,85112
Non-polymers3356
Water25,8341434
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)588,37136
Polymers587,70124
Non-polymers67012
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)197.170, 127.030, 134.180
Angle α, β, γ (deg.)90.00, 97.64, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(0.23759137, 0.91398592, -0.05616918), (0.24412326, 0.9698113), (1.00499337, -0.23007076, -0.23759137)
2given(0.22312522, 0.23007805, 0.88639387), (1.03265551, -0.244131), (-0.05616562, 0.97321262, -0.22312522)
3given(-0.88766519, 0.44626459), (-1), (0.47516768, 0.88766519)
4given(0.23759137, -0.91398592, -0.05616918), (-0.24412326, -0.9698113), (1.00499337, 0.23007076, -0.23759137)
5given(-0.22312522, 0.23007805, -0.88639387), (-1.03265551, 0.244131), (0.05616562, 0.97321262, 0.22312522)

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Components

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


Mass: 22278.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria)
References: UniProt: P00436, protocatechuate 3,4-dioxygenase
#2: Protein
PROTOCATECHUATE 3,4-DIOXYGENASE (BETA CHAIN)


Mass: 26696.287 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1434 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIF ALL THE COORDINATES FOR THE SIX PROTOMERS ARE AVERAGED, THE RMS DEVIATION OF EACH PROTOMER FROM ...IF ALL THE COORDINATES FOR THE SIX PROTOMERS ARE AVERAGED, THE RMS DEVIATION OF EACH PROTOMER FROM THE MEAN, USING ALL ATOMS (PROTEIN + FE + WATER), IS PROTOMER DEVIATION A 0.1860 B 0.1942 C 0.1712 D 0.1922 E 0.1802 F 0.2094 TURNS HAVE BEEN CLASSIFIED AS SUGGESTED BY SIBANDA, B.L., BLUNDELL, T.L., & THORNTON, J.M. (1989). J. MOL. BIOL. 206, 759-777. LETTERS REFER TO REGIONS OF RAMACHANDRAN PLOT AS DESCRIBED BY EFIMOV. B = BETA, AR = RIGHT-HANDED ALPHA, AL = LEFT-HANDED ALPHA, GR = RIGHT-HANDED GAMMA, GL = LEFT- HANDED GAMMA, D = DELTA, AND E = EPSILON. HELIX 1 AA TYR A 16 ALA A 22 1 HELIX A, PROTOMER A
Sequence detailsTHE SEQUENCE PRESENTED IN THIS ENTRY IS BASED ON THE NUCLEOTIDE SEQUENCE PRESENTED IN GENBANK ENTRY ...THE SEQUENCE PRESENTED IN THIS ENTRY IS BASED ON THE NUCLEOTIDE SEQUENCE PRESENTED IN GENBANK ENTRY L14836 AND PUBLISHED IN R.W.FRAZEE, D.M.LIVINGSTON, D.C.LAPORTE, AND J.D.LIPSCOMB, (1993) CLONING, SEQUENCING, AND EXPRESSION OF THE PSEUDOMONAS PUTIDA PROTOCATECHUATE 3, 4 - DIOXYGENASE GENES. J. BACTERIOL. 175, 6194 - 6202. PIR ENTRIES DAPSAA AND DAPSBA ARE FROM THE AMINO ACID SEQUENCES OF THE ALPHA AND BETA CHAINS, RESPECTIVELY. THE FOLLOWING ARE THE DIFFERENCES BETWEEN THESE SEQUENCES: RESIDUE PIR GENBANK 59 ASP ASN 76 ASP ASN 361 ASP HIS 369 ASP ASN 370 - GLY 517 ASN ASP CROSS REFERENCE TO SEQUENCE DATABASE SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME PCXA_PSEAE A PCXA_PSEAE B PCXA_PSEAE C PCXA_PSEAE D PCXA_PSEAE E PCXA_PSEAE F PCXB_PSEAE M PCXB_PSEAE N PCXB_PSEAE O PCXB_PSEAE P PCXB_PSEAE Q PCXB_PSEAE R SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PCXA_PSEAE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 59 ASN A 59 ASP 76 ASN A 76 ASP 59 ASN B 59 ASP 76 ASN B 76 ASP 59 ASN C 59 ASP 76 ASN C 76 ASP 59 ASN D 59 ASP 76 ASN D 76 ASP 59 ASN E 59 ASP 76 ASN E 76 ASP 59 ASN F 59 ASP 76 ASN F 76 SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PCXB_PSEAE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 61 HIS M 361 ASN 216 ASP M 517 ASP 61 HIS N 361 ASN 216 ASP N 517 ASP 61 HIS O 361 ASN 216 ASP O 517 ASP 61 HIS P 361 ASN 216 ASP P 517 ASP 61 HIS Q 361 ASN 216 ASP Q 517 ASP 61 HIS R 361 ASN 216 ASP R 517 RESIDUES OF CHAIN M MISSING FROM THE ATOM LIST SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 68 ASP 69 RESIDUES OF CHAIN M MISSING THE C-TERMINUS SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 236 CYS 237 RESIDUES OF CHAIN N MISSING FROM THE ATOM LIST SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 68 ASP 69 RESIDUES OF CHAIN N MISSING THE C-TERMINUS SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 236 CYS 237 RESIDUES OF CHAIN O MISSING FROM THE ATOM LIST SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 68 ASP 69 RESIDUES OF CHAIN O MISSING THE C-TERMINUS SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 236 CYS 237 RESIDUES OF CHAIN P MISSING FROM THE ATOM LIST SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 68 ASP 69 RESIDUES OF CHAIN P MISSING THE C-TERMINUS SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 236 CYS 237 RESIDUES OF CHAIN Q MISSING FROM THE ATOM LIST SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 68 ASP 69 RESIDUES OF CHAIN Q MISSING THE C-TERMINUS SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 236 CYS 237 RESIDUES OF CHAIN R MISSING FROM THE ATOM LIST SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 68 ASP 69 RESIDUES OF CHAIN R MISSING THE C-TERMINUS SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 236 CYS 237

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.4 / Method: free interface diffusion / Details: or hanging drop vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-75 mg/mlprotein11
21.5-1.8 Mammonium sulfate12
350 mMTris-HCl12
410 mMbeta-mercaptoethanol12

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Data collection

ReflectionNum. obs: 164157 / % possible obs: 95.7 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.15→5 Å / σ(F): 0
Details: THIS NONSTANDARD UNIT CELL WAS CHOSEN OVER THE EQUIVALENT C2 CELL (A = 223.26, B = 127.03, C = 134.18, BETA = 61.08) BECAUSE OF THE CONVENIENCE OF HAVING A BETA ANGLE NEAR 90 DEGREES AND TO ...Details: THIS NONSTANDARD UNIT CELL WAS CHOSEN OVER THE EQUIVALENT C2 CELL (A = 223.26, B = 127.03, C = 134.18, BETA = 61.08) BECAUSE OF THE CONVENIENCE OF HAVING A BETA ANGLE NEAR 90 DEGREES AND TO MAINTAIN CONSISTENCY WITH THE INITIAL CRYSTALLIZATION REPORT. TO CONVERT FROM FRAC_I2 TO FRAC_C2 USE THE FOLLOWING: [ 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 COORDINATES HAVE BEEN DEPOSITED IN THE ORTHOGONAL COORDINATES DEFINED BY THE LOCAL SYMMETRY OF THE COMPLEX (23). DURING REFINEMENT THE THERMAL FACTORS OF ATOMS THAT ARE HYDROGEN BONDED TO EACH OTHER WERE RESTRAINED TO BE SIMILAR. THE OCCUPANCIES OF THE SOLVENTS WERE ALLOWED TO VARY ONLY IN STEPS OF 0.200. BEFORE THE GENERATION OF A MAP THE OCCUPANCIES OF NCS-RELATED SOLVENTS WERE AVERAGED AND QUANTIZED TO A MULTIPLE OF 0.100.
RfactorNum. reflection
obs0.172 136440
Refinement stepCycle: LAST / Resolution: 2.15→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20466 0 6 1434 21906
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.03
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.5071
X-RAY DIFFRACTIONp_mcangle_it0.8992
X-RAY DIFFRACTIONp_scbond_it1.0971.5
X-RAY DIFFRACTIONp_scangle_it1.8223
X-RAY DIFFRACTIONp_plane_restr0.0130.03
X-RAY DIFFRACTIONp_chiral_restr0.2270.3
X-RAY DIFFRACTIONp_singtor_nbd0.180.5
X-RAY DIFFRACTIONp_multtor_nbd0.2120.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1550.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.23
X-RAY DIFFRACTIONp_staggered_tor17.215
X-RAY DIFFRACTIONp_orthonormal_tor23.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection all: 136440 / Rfactor all: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS

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