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- PDB-3lkt: Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficien... -

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Entry
Database: PDB / ID: 3lkt
TitleTyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Components(Protocatechuate 3,4-dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / Protocatechuate / dioxygenase / non-heme / Y447H / iron-dependent / Aromatic hydrocarbons catabolism / Iron / Metal-binding
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 / molecular replacement / Resolution: 1.65 Å
AuthorsLipscomb, J.D. / Purpero, V.M.
CitationJournal: To be Published
Title: Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Authors: Purpero, V.M. / Valley, M.P. / Ohlendorf, D.H. / Lipscomb, J.D. / Burk, D. / Dolbeare, K.B. / Brown, K.C.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 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_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.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_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.pdbx_ptnr2_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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)298,22672
Polymers293,70012
Non-polymers4,52660
Water49,7032759
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)596,452144
Polymers587,40124
Non-polymers9,051120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area162250 Å2
ΔGint-1018 kcal/mol
Surface area169630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.310, 168.040, 128.160
Angle α, β, γ (deg.)90.00, 132.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-2079-

HOH

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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) / Gene: pcaG / 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: 26671.260 Da / Num. of mol.: 6 / Mutation: Y447H
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, 2819 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-FE / FE (III) ION


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


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2759 / 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: 52.33 %
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 buffer, pH 8.5, 5 mM BME, 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 23, 2009 / Details: vertical focusing mirror
RadiationMonochromator: Sagitally focusing crystal and a double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 357899 / Num. obs: 351447 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.9 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.32 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.42 Å
Translation2.5 Å41.42 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHASER generated pdb

Resolution: 1.65→29.57 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.366 / SU ML: 0.048 / SU R Cruickshank DPI: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17344 17717 5 %RANDOM
Rwork0.14831 ---
obs0.14959 333726 98.22 %-
all-357899 --
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 mean: 20.377 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20736 0 225 2759 23720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02221772
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.94829622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41752684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43423.751104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.443153304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.44215173
X-RAY DIFFRACTIONr_chiral_restr0.0990.23117
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117215
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6981.513316
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.268221525
X-RAY DIFFRACTIONr_scbond_it1.99538456
X-RAY DIFFRACTIONr_scangle_it3.2154.58079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.647→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 1213 -
Rwork0.188 23579 -
obs--94.02 %

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