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- PDB-1ykn: Protocatechuate 3,4-dioxygenase Y408E mutant bound to DHB -

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Basic information

Entry
Database: PDB / ID: 1ykn
TitleProtocatechuate 3,4-dioxygenase Y408E mutant bound to DHB
Components
  • Protocatechuate 3,4-dioxygenase alpha chain
  • Protocatechuate 3,4-dioxygenase beta chain
KeywordsOXIDOREDUCTASE / catechol / 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 / Intradiol ring-cleavage dioxygenases signature. / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase ...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 / Intradiol ring-cleavage dioxygenases signature. / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Sandwich / Mainly Beta
Similarity search - Domain/homology
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 / FOURIER SYNTHESIS / Resolution: 2.06 Å
AuthorsBrown, C.K. / Ohlendorf, D.H.
CitationJournal: Biochemistry / Year: 2005
Title: Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis
Authors: Valley, M.P. / Brown, C.K. / Burk, D.L. / Vetting, M.W. / Ohlendorf, D.H. / Lipscomb, J.D.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 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_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.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.value / _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_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 beta chain
C: Protocatechuate 3,4-dioxygenase alpha chain
D: Protocatechuate 3,4-dioxygenase beta chain
E: Protocatechuate 3,4-dioxygenase alpha chain
F: Protocatechuate 3,4-dioxygenase beta chain
G: Protocatechuate 3,4-dioxygenase alpha chain
H: Protocatechuate 3,4-dioxygenase beta chain
I: Protocatechuate 3,4-dioxygenase alpha chain
J: Protocatechuate 3,4-dioxygenase beta chain
K: Protocatechuate 3,4-dioxygenase alpha chain
L: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,36324
Polymers294,10312
Non-polymers1,26012
Water27,2391512
1
A: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase beta chain
C: Protocatechuate 3,4-dioxygenase alpha chain
D: Protocatechuate 3,4-dioxygenase beta chain
E: Protocatechuate 3,4-dioxygenase alpha chain
F: Protocatechuate 3,4-dioxygenase beta chain
G: Protocatechuate 3,4-dioxygenase alpha chain
H: Protocatechuate 3,4-dioxygenase beta chain
I: Protocatechuate 3,4-dioxygenase alpha chain
J: Protocatechuate 3,4-dioxygenase beta chain
K: Protocatechuate 3,4-dioxygenase alpha chain
L: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

A: Protocatechuate 3,4-dioxygenase alpha chain
B: Protocatechuate 3,4-dioxygenase beta chain
C: Protocatechuate 3,4-dioxygenase alpha chain
D: Protocatechuate 3,4-dioxygenase beta chain
E: Protocatechuate 3,4-dioxygenase alpha chain
F: Protocatechuate 3,4-dioxygenase beta chain
G: Protocatechuate 3,4-dioxygenase alpha chain
H: Protocatechuate 3,4-dioxygenase beta chain
I: Protocatechuate 3,4-dioxygenase alpha chain
J: Protocatechuate 3,4-dioxygenase beta chain
K: Protocatechuate 3,4-dioxygenase alpha chain
L: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)590,72548
Polymers588,20624
Non-polymers2,52024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area144790 Å2
ΔGint-767 kcal/mol
Surface area168410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)195.821, 128.569, 134.356
Angle α, β, γ (deg.)90.00, 97.98, 90.00
Int Tables number5
Space group name H-MI121

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Components

#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) / Gene: pcaG / Production host: Escherichia coli (E. coli)
References: UniProt: P00436, protocatechuate 3,4-dioxygenase
#2: Protein
Protocatechuate 3,4-dioxygenase beta chain / 3 / 4-PCD


Mass: 26738.344 Da / Num. of mol.: 6 / Mutation: Y408E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Production host: Escherichia coli (E. coli)
References: UniProt: P00437, protocatechuate 3,4-dioxygenase
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID / Protocatechuic acid


Mass: 154.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H6O4
#5: Water ChemComp-HOH / water / 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: 2.85 Å3/Da / Density % sol: 56.77 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 8.3 Å2

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.06→8.51 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 98076.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1265 0.9 %RANDOM
Rwork0.149 ---
obs0.149 138492 69.6 %-
all-146121 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.8871 Å2 / ksol: 0.448385 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å2-0.83 Å2
2--1.35 Å20 Å2
3---1.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.06→8.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20682 0 72 1512 22266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.046
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg3.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 24 0.9 %
Rwork0.347 2690 -
obs--7.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2iron.param
X-RAY DIFFRACTION3cyc.kent.param
X-RAY DIFFRACTION4dhb.par
X-RAY DIFFRACTION5water_rep.param

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