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- PDB-3t63: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleava... -

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Basic information

Entry
Database: PDB / ID: 3t63
TitleAxial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Components(Protocatechuate 3,4-dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / iron III dependent non-heme intradiol dioxygenase
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 / : / 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 / Resolution: 1.54 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
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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

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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)148,58229
Polymers146,7246
Non-polymers1,85823
Water27,2391512
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)594,327116
Polymers586,89624
Non-polymers7,43192
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 area158120 Å2
ΔGint-975 kcal/mol
Surface area168650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.119, 140.618, 167.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11O-950-

HOH

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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 / Plasmid: pVMP001 / 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: 26629.219 Da / Num. of mol.: 3 / Mutation: Y447A/H462Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pVMP001 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00437, protocatechuate 3,4-dioxygenase

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Non-polymers , 5 types, 1535 molecules

#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1512 / 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: 52.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5-1.8 M ammonium sulfate, 5 mM BME, 40-60 mM Tris, pH 8.5, varying ML:ENZ ratios from 1:2 to 4:1, 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: Oct 24, 2009 / Details: mirrors
RadiationMonochromator: Sagitally focused double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. all: 233264 / Num. obs: 218848 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.049 / Χ2: 1.078 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.54-1.575.20.423107720.831198.5
1.57-1.65.50.376108670.828199.2
1.6-1.635.50.318109110.854199.6
1.63-1.665.60.285109260.875199.5
1.66-1.695.60.241109250.893199.5
1.69-1.735.60.199109300.907199.6
1.73-1.785.60.164109480.935199.7
1.78-1.835.60.135109470.971199.8
1.83-1.885.60.112109501.021199.8
1.88-1.945.60.091109711.087199.8
1.94-2.015.60.074109931.138199.8
2.01-2.095.60.065109661.199199.8
2.09-2.195.60.055110221.296199.9
2.19-2.35.60.047110201.352199.8
2.3-2.445.60.044109681.407199.6
2.44-2.635.60.039110141.515199.3
2.63-2.95.60.036109591.285198.9
2.9-3.325.50.032109561.068198.5
3.32-4.185.40.028109131.037197.5
4.18-505.20.028108900.999194.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PCD CHAINS A/M, B/N, C/O

2pcd


Resolution: 1.54→29.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1768 / WRfactor Rwork: 0.1539 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9032 / SU B: 1.067 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0675 / SU Rfree: 0.0677 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 10986 5 %RANDOM
Rwork0.1551 ---
obs0.1562 207805 99.01 %-
all-218836 --
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: 52.45 Å2 / Biso mean: 19.9284 Å2 / Biso min: 11.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.54→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10359 0 95 1512 11966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210934
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9514892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41651354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59323.8550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.413151661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8461586
X-RAY DIFFRACTIONr_chiral_restr0.0980.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218674
X-RAY DIFFRACTIONr_mcbond_it0.7081.56699
X-RAY DIFFRACTIONr_mcangle_it1.279210842
X-RAY DIFFRACTIONr_scbond_it1.97334235
X-RAY DIFFRACTIONr_scangle_it3.2084.54045
LS refinement shellResolution: 1.542→1.582 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 774 -
Rwork0.186 14927 -
all-15701 -
obs-14927 96.84 %

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