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- PDB-3mv6: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleava... -

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Basic information

Entry
Database: PDB / ID: 3mv6
TitleAxial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Components(Protocatechuate 3,4-dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / intradiol / dioxygenase / ES 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
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 / 3,4-DIHYDROXYBENZOIC ACID / : / 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: 1.86 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
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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
B: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
M: Protocatechuate 3,4-dioxygenase beta chain
N: Protocatechuate 3,4-dioxygenase beta chain
O: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,00829
Polymers146,9256
Non-polymers2,08323
Water16,862936
1
A: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
M: Protocatechuate 3,4-dioxygenase beta chain
N: Protocatechuate 3,4-dioxygenase beta chain
O: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

A: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
M: Protocatechuate 3,4-dioxygenase beta chain
N: Protocatechuate 3,4-dioxygenase beta chain
O: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

A: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
M: Protocatechuate 3,4-dioxygenase beta chain
N: Protocatechuate 3,4-dioxygenase beta chain
O: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

A: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
M: Protocatechuate 3,4-dioxygenase beta chain
N: Protocatechuate 3,4-dioxygenase beta chain
O: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)596,033116
Polymers587,70124
Non-polymers8,33192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area159420 Å2
ΔGint-1169 kcal/mol
Surface area166990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.142, 140.831, 167.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsThe alpha-beta subunits are not covalently linked, making a 24-mer as a biological assembly in solution (12 ab, dodecamer). Applying the symmetry operators (-x,-y,z), (-x, y,-z) and (x,-y,-z) to (x,y,z) yields the biological assembly.

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Components

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Protocatechuate 3,4-dioxygenase ... , 2 types, 6 molecules ABCMNO

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


Mass: 22278.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaG, pcaH / Plasmid: pCE025 / 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.: 3 / Mutation: Y148H/H163Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pCE025 / 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, 959 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 936 / 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: 52.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5-1.8 M ammonium sulfate, 40-60 mM TRIS-HCl pH 8.5, and 2-10 mM beta-mercaptoethanol, 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 315r / Detector: CCD / Date: Apr 16, 2009 / Details: mirrors
RadiationMonochromator: sagitally focused double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 120737 / Num. obs: 120737 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.126 / Χ2: 1.183 / Net I/σ(I): 9.8
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.55 / Num. unique all: 6140 / Χ2: 1.008 / % possible all: 98

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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
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→29.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.854 / SU B: 2.629 / SU ML: 0.08 / SU R Cruickshank DPI: 0.144 / SU Rfree: 0.134 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.219 6067 5 %RANDOM
Rwork0.181 ---
all0.183 120737 --
obs0.183 120248 94.69 %-
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: 63.68 Å2 / Biso mean: 25.35 Å2 / Biso min: 3.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.86→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 114 936 11424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210877
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.95314830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47551345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61123.745550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.557151662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9621586
X-RAY DIFFRACTIONr_chiral_restr0.1120.21559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218619
X-RAY DIFFRACTIONr_mcbond_it0.7721.56630
X-RAY DIFFRACTIONr_mcangle_it1.373210717
X-RAY DIFFRACTIONr_scbond_it2.25734247
X-RAY DIFFRACTIONr_scangle_it3.5794.54094
LS refinement shellResolution: 1.859→1.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 413 -
Rwork0.228 8010 -
all-8423 -
obs-6067 90.82 %

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