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Open data
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Basic information
Entry | Database: PDB / ID: 3pcd | |||||||||
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Title | PROTOCATECHUATE 3,4-DIOXYGENASE Y447H MUTANT | |||||||||
![]() | (PROTOCATECHUATE 3,4- ...) x 2 | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Orville, A.M. / Lipscomb, J.D. / Ohlendorf, D.H. | |||||||||
![]() | ![]() Title: The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates. Authors: Frazee, R.W. / Orville, A.M. / Dolbeare, K.B. / Yu, H. / Ohlendorf, D.H. / Lipscomb, J.D. #1: ![]() Title: Crystal Structure and Resonance Raman Studies of Protocatechuate 3,4-Dioxygenase Complexed with 3,4-Dihydroxyphenylacetate Authors: Elgren, T.E. / Orville, A.M. / Kelly, K.A. / Lipscomb, J.D. / Ohlendorf, D.H. / Que Junior, L. #2: ![]() 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. #3: ![]() 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. #4: ![]() 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. #5: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 540.6 KB | Display | ![]() |
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PDB format | ![]() | 438.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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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 |
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Components
-PROTOCATECHUATE 3,4- ... , 2 types, 12 molecules ABCDEFMNOPQR
#1: Protein | ![]() Mass: 22278.812 Da / Num. of mol.: 6 / Mutation: Y447H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00436, ![]() #2: Protein | ![]() Mass: 26671.260 Da / Num. of mol.: 6 / Mutation: Y447H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00437, ![]() |
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-Non-polymers , 4 types, 1440 molecules ![](data/chem/img/CO3.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CO3 / ![]() #4: Chemical | ChemComp-FE / ![]() #5: Chemical | ChemComp-BME / ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Nonpolymer details | CARBONATE (RESIDUE 550) IS OBSERVED BOUND TO THE FE(III). |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.83 % | |||||||||||||||||||||||||
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Crystal grow![]() | pH: 8.4 / Details: pH 8.4 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 21, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→10 Å / Num. obs: 161689 / % possible obs: 78 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rsym value: 0.107 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.04→2.17 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 1 / % possible all: 51 |
Reflection | *PLUS Num. measured all: 333815 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 51 % / Rmerge(I) obs: 0.107 |
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Processing
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Refinement | Method to determine structure![]() 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: 19.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rfactor obs: 0.25 |