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- PDB-4whq: Alkylperoxo reaction intermediate trapped in Protocatechuate 3,4-... -

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Basic information

Entry
Database: PDB / ID: 4whq
TitleAlkylperoxo reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5
Components(Protocatechuate 3,4-dioxygenase ...) x 2
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 / 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
4-fluorobenzene-1,2-diol / Chem-3N9 / 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 / Resolution: 1.78 Å
AuthorsKnoot, C.J. / Purpero, V.M. / 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_validate_close_contact / 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 1.5Dec 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

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


Theoretical massNumber of molelcules
Total (without water)150,55644
Polymers146,9256
Non-polymers3,63138
Water16,051891
1
A: Protocatechuate 3,4-dioxygenase alpha chain
E: Protocatechuate 3,4-dioxygenase alpha chain
F: Protocatechuate 3,4-dioxygenase beta chain
C: Protocatechuate 3,4-dioxygenase alpha chain
D: Protocatechuate 3,4-dioxygenase beta chain
B: Protocatechuate 3,4-dioxygenase beta chain
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)602,225176
Polymers587,70124
Non-polymers14,524152
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 area156610 Å2
ΔGint-980 kcal/mol
Surface area165310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.259, 140.724, 167.824
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-724-

HOH

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Components

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

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


Mass: 26696.287 Da / Num. of mol.: 3
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 , 10 types, 929 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-3N8 / 4-fluorobenzene-1,2-diol


Mass: 128.101 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C6H5FO2
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#6: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#7: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-3N9 / (6S)-4-fluoro-6-hydroperoxy-6-hydroxycyclohexa-2,4-dien-1-one


Mass: 160.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5FO4
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 891 / 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: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.2 M Ammonium Sulfate, 2.5 mM 2-mercaptoethanol, 100 mM MES pH 6.5; 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: 1.78→50 Å / Num. obs: 140459 / % possible obs: 97.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.036 / Rrim(I) all: 0.082 / Χ2: 2.463 / Net I/av σ(I): 30.842 / Net I/σ(I): 16.4 / Num. measured all: 671887
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.814.10.47969290.8110.2550.5471.00997.2
1.81-1.844.50.44569870.8540.230.5041.03298.3
1.84-1.884.60.36470300.8960.1860.4111.1198.7
1.88-1.924.70.31371060.9120.160.3541.2799.1
1.92-1.964.70.2670500.9320.1320.2931.37299.4
1.96-24.80.22371240.9470.1120.2511.54199.5
2-2.054.80.19771060.9560.0990.2211.64499.5
2.05-2.114.80.16871290.9690.0850.1891.87599.7
2.11-2.174.80.14771190.9750.0730.1652.10399.8
2.17-2.244.80.12471710.9810.0620.1392.36399.9
2.24-2.324.90.11371420.9830.0570.1272.52699.8
2.32-2.424.90.10171530.9870.050.1142.60399.8
2.42-2.534.90.0971650.9890.0450.1012.88199.8
2.53-2.664.90.07971860.9920.0390.0883.09599.8
2.66-2.8350.07271800.9930.0350.0813.4299.8
2.83-3.0450.06671520.9940.0320.0743.88199.4
3.04-3.3550.06471400.9930.0310.0714.62598.4
3.35-3.834.80.05268150.9940.0260.0594.11793.9
3.83-4.834.60.03862320.9960.020.0433.04785.3
4.83-5050.03765430.9970.0180.0413.00586.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.78→39.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1868 / WRfactor Rwork: 0.1611 / FOM work R set: 0.8816 / SU B: 2.067 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1093 / SU Rfree: 0.1049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 7059 5 %RANDOM
Rwork0.1643 133369 --
obs0.1658 133369 97.53 %-
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: 85.75 Å2 / Biso mean: 27.162 Å2 / Biso min: 15.54 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.78→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10357 0 226 891 11474
Biso mean--45.43 32.44 -
Num. residues----1312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910925
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210066
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.96614868
X-RAY DIFFRACTIONr_angle_other_deg0.8183.00123068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68351319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34123.736546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.882151636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9271584
X-RAY DIFFRACTIONr_chiral_restr0.0980.21542
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022691
LS refinement shellResolution: 1.78→1.829 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 473 -
Rwork0.209 9653 -
all-10126 -
obs--96.09 %

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