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Basic information

Entry
Database: PDB / ID: 3mi5
TitleAxial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Components(Protocatechuate 3,4-dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / dioxygenase / non-heme / iron / intradiol / catechol / substrate analogue / protocatechuate
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
BETA-MERCAPTOETHANOL / CATECHOL / : / Protocatechuate 3,4-dioxygenase alpha chain / Protocatechuate 3,4-dioxygenase beta chain
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsPurpero, V.M. / Lipscomb, J.D.
CitationJournal: To be Published
Title: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Authors: Purpero, V.M. / Lipscomb, J.D.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 6, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)302,658114
Polymers293,85112
Non-polymers8,808102
Water41,4352300
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)605,317228
Polymers587,70124
Non-polymers17,615204
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area189900 Å2
ΔGint-1243 kcal/mol
Surface area161300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.543, 167.995, 128.342
Angle α, β, γ (deg.)90.000, 132.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-1874-

HOH

Detailsexists as a dodecamer (12) of dimer in solution. The space group C2 shows 6 of 12 (x,y,z). By applying the symmetry operator (-x,-y,-z) this completes the biological unit assembly.

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Components

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Protocatechuate 3,4-dioxygenase ... , 2 types, 12 molecules ABCDEFMNOPQR

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


Mass: 22278.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: P. putida / Gene: pcaG / Plasmid: pCE vector, pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P00436, protocatechuate 3,4-dioxygenase
#2: Protein
Protocatechuate 3,4-dioxygenase beta chain / 3 / 4-PCD


Mass: 26696.287 Da / Num. of mol.: 6 / Mutation: Y148H/H163Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pCE vector, pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P00437, protocatechuate 3,4-dioxygenase

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Non-polymers , 7 types, 2402 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H6O2
#7: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2300 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5-1.8 M ammounium sulfate, 40-60 mM TRIS pH 8.5, 5 mM BME protein conc. 15-25 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 15, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 284851 / Num. obs: 282736 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 5 / Redundancy: 3 % / Biso Wilson estimate: 19.77 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.16 / Net I/σ(I): 15.5
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.76 / Num. unique all: 14065 / Χ2: 1.111 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→30.62 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.15 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.89 / SU B: 2.009 / SU ML: 0.064 / SU R Cruickshank DPI: 0.103 / SU Rfree: 0.101 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 3 / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.185 14311 5.1 %RANDOM
Rwork0.151 ---
all0.186 284851 --
obs0.153 282689 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 70.21 Å2 / Biso mean: 21.401 Å2 / Biso min: 4.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.04 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.78→30.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20748 0 519 2300 23567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02222418
X-RAY DIFFRACTIONr_angle_refined_deg1.371.96130504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26352786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8823.8851148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.726153404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.63315177
X-RAY DIFFRACTIONr_chiral_restr0.1060.23158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117693
X-RAY DIFFRACTIONr_mcbond_it0.7211.513415
X-RAY DIFFRACTIONr_mcangle_it1.301221753
X-RAY DIFFRACTIONr_scbond_it2.10839003
X-RAY DIFFRACTIONr_scangle_it3.4084.58676
LS refinement shellResolution: 1.777→1.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 1032 -
Rwork0.208 19222 -
all-20254 -
obs-14311 96.5 %

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