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- PDB-4who: Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 4who
TitleResting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5
Components
  • (Protocatechuate 3,4-dioxygenase beta ...) x 2
  • Protocatechuate 3,4-dioxygenase alpha chain
KeywordsOXIDOREDUCTASE / dioxygen activation / non-heme iron / intradiol dioxygenase / aromatic ring cleavage / catalytic intermediates
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
BICARBONATE ION / 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: 1.83 Å
AuthorsKnoot, C.J. / Lipscomb, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM24689 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08700 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.
Authors: Knoot, C.J. / Purpero, V.M. / Lipscomb, J.D.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...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 / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
E: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase beta chain
D: Protocatechuate 3,4-dioxygenase beta chain
F: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,32612
Polymers146,9416
Non-polymers3856
Water16,502916
1
A: Protocatechuate 3,4-dioxygenase alpha chain
E: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase beta chain
D: Protocatechuate 3,4-dioxygenase beta chain
F: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

A: Protocatechuate 3,4-dioxygenase alpha chain
E: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase beta chain
D: Protocatechuate 3,4-dioxygenase beta chain
F: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

A: Protocatechuate 3,4-dioxygenase alpha chain
E: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase beta chain
D: Protocatechuate 3,4-dioxygenase beta chain
F: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

A: Protocatechuate 3,4-dioxygenase alpha chain
E: Protocatechuate 3,4-dioxygenase alpha chain
C: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase beta chain
D: Protocatechuate 3,4-dioxygenase beta chain
F: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)589,30448
Polymers587,76524
Non-polymers1,53924
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 area139280 Å2
ΔGint-791 kcal/mol
Surface area170930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.092, 140.636, 168.660
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
11F-714-

HOH

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Components

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Protein , 1 types, 3 molecules AEC

#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: pCE120K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00436, protocatechuate 3,4-dioxygenase

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Protocatechuate 3,4-dioxygenase beta ... , 2 types, 3 molecules BDF

#2: Protein Protocatechuate 3,4-dioxygenase beta chain / 3 / 4-PCD


Mass: 26712.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pCE120K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00437, protocatechuate 3,4-dioxygenase
#3: Protein Protocatechuate 3,4-dioxygenase beta chain / 3 / 4-PCD


Mass: 26696.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pCE120K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00437, protocatechuate 3,4-dioxygenase

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Non-polymers , 4 types, 922 molecules

#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 52.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2 M Ammonium Sulfate, 2.5 mM 2-mercaptoethanol, 100 mM Tris-HCl pH 8.5; 2:1 ratio of well sol. to 40 mg/ml protein solution in drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 121908 / % possible obs: 90.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.086 / Rrim(I) all: 0.184 / Χ2: 7.365 / Net I/av σ(I): 24.779 / Net I/σ(I): 13.1 / Num. measured all: 559978
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.864.60.45366290.8480.2360.5131.74699.9
1.86-1.94.70.39566650.8880.2040.4452.01699.9
1.9-1.934.70.34966510.9020.1790.3942.27999.9
1.93-1.974.70.30366080.9170.1560.3422.76399.9
1.97-2.014.70.26866770.9220.1380.3033.28100
2.01-2.064.80.24966620.9320.1280.283.63499.9
2.06-2.114.70.22266480.9390.1150.2514.21899.9
2.11-2.174.80.20366420.9430.1050.235.05699.9
2.17-2.234.70.18666860.9470.0970.216.15499.8
2.23-2.314.70.17866220.9480.0930.2026.94599.5
2.31-2.394.70.17166070.9510.0890.1937.7399.2
2.39-2.484.70.16466220.9510.0860.1868.60998.6
2.48-2.64.60.15865260.9460.0840.1810.5297.3
2.6-2.734.60.15164120.9530.0810.17211.50596.2
2.73-2.94.50.14262400.950.0770.16212.56892.7
2.9-3.134.40.13158350.9540.0720.1513.5286.9
3.13-3.444.10.1250520.9560.0680.13814.88574.8
3.44-3.9440.10941600.9550.0620.12716.31961.7
3.94-4.9740.09733470.9630.0550.11217.22149.1
4.97-504.30.07646170.9810.0410.08714.23365.6

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Processing

Software
NameVersionClassification
HKL-3000data reduction
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T63

3t63


Resolution: 1.83→32.45 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2108 / WRfactor Rwork: 0.1762 / FOM work R set: 0.878 / SU B: 2.183 / SU ML: 0.068 / SU R Cruickshank DPI: 0.139 / SU Rfree: 0.1299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 6094 5 %RANDOM
Rwork0.1801 115055 --
obs0.1819 115055 90.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 71.05 Å2 / Biso mean: 22.134 Å2 / Biso min: 12.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.05 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.83→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10338 0 15 916 11269
Biso mean--34.48 27.46 -
Num. residues----1309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910635
X-RAY DIFFRACTIONr_bond_other_d0.0020.029907
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.94414479
X-RAY DIFFRACTIONr_angle_other_deg0.824322724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53151303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78123.734541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.153151623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3461584
X-RAY DIFFRACTIONr_chiral_restr0.1010.21528
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022613
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 474 -
Rwork0.188 9087 -
all-9561 -
obs--98.17 %

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