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Yorodumi- PDB-3pcf: STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-FLU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pcf | |||||||||
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Title | STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-FLURO-4-HYDROXYBENZOATE | |||||||||
Components | (PROTOCATECHUATE 3,4- ...) x 2 | |||||||||
Keywords | DIOXYGENASE / IRON / NONHEME / METALLOPROTEIN / OXIDOREDUCTASE / INHIBITOR COMPLEX | |||||||||
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 | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / NATIVE MODEL PHASES / Resolution: 2.15 Å | |||||||||
Authors | Orville, A.M. / Elango, N. / 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: 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. #2: 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. #3: Journal: Nature / Year: 1988 Title: Structure and Assembly of Protocatechuate 3,4-Dioxygenase Authors: Ohlendorf, D.H. / Lipscomb, J.D. / Weber, P.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pcf.cif.gz | 545.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pcf.ent.gz | 442.7 KB | Display | PDB format |
PDBx/mmJSON format | 3pcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pcf_validation.pdf.gz | 481.5 KB | Display | wwPDB validaton report |
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Full document | 3pcf_full_validation.pdf.gz | 571.8 KB | Display | |
Data in XML | 3pcf_validation.xml.gz | 62.6 KB | Display | |
Data in CIF | 3pcf_validation.cif.gz | 99.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/3pcf ftp://data.pdbj.org/pub/pdb/validation_reports/pc/3pcf | HTTPS FTP |
-Related structure data
Related structure data | 3pcbC 3pccC 3pceC 3pcgC 3pchC 3pciC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE 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 |
-Components
-PROTOCATECHUATE 3,4- ... , 2 types, 12 molecules ABCDEFMNOPQR
#1: Protein | 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 | 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, 1476 molecules
#3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-BME / #5: Chemical | ChemComp-FHB / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE INHIBITOR IS OBSERVED IN TWO BINDING SITES. THE FIRST IS IN THE ACTIVE SITE OF EACH PROTOMER ...THE INHIBITOR IS OBSERVED IN TWO BINDING SITES. THE FIRST IS IN THE ACTIVE SITE OF EACH PROTOMER (RESIDUE 550). THE SECOND IS AT EACH LOCAL THREE-FOLD SYMMETRY AXES (RESIDUE 551). THE SECONDARY BINDING SITES ARE DEFINED BY: S2M AND S2P. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.22 % | |||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 5, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→10 Å / Num. obs: 167068 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rsym value: 0.102 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.14→2.27 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.2 / % possible all: 83 |
Reflection | *PLUS Num. measured all: 469264 / Rmerge(I) obs: 0.102 |
Reflection shell | *PLUS % possible obs: 83 % |
-Processing
Software |
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Refinement | Method to determine structure: NATIVE MODEL PHASES / Resolution: 2.15→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).
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Displacement parameters | Biso mean: 22.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor obs: 0.236 |