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- PDB-4whp: Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 4whp
TitleResting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5
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: 1.541 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: 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_symm_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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _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.number_atoms_total / _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

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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)147,53614
Polymers146,9416
Non-polymers5958
Water20,1051116
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)590,14556
Polymers587,76524
Non-polymers2,37932
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 area142450 Å2
ΔGint-1026 kcal/mol
Surface area171890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.919, 140.767, 168.191
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-719-

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 FDB

#2: 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
#3: 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

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Non-polymers , 5 types, 1124 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
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: 1.54→50 Å / Num. obs: 206314 / % possible obs: 93.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.061 / Rrim(I) all: 0.139 / Χ2: 4.061 / Net I/av σ(I): 29.661 / Net I/σ(I): 12.1 / Num. measured all: 1026896
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.54-1.573.70.475109560.8320.2770.5521.033100
1.57-1.64.20.469109470.8420.2540.5351.082100
1.6-1.634.60.428109830.8790.220.4831.184100
1.63-1.664.90.402109790.9050.1980.451.262100
1.66-1.695.10.359109750.9180.1730.3991.4100
1.69-1.735.20.315110020.9360.1490.3491.651100
1.73-1.785.30.274109740.9450.1290.3032.036100
1.78-1.835.30.237109830.9540.1110.2622.434100
1.83-1.885.40.21109830.9630.0990.2322.95999.9
1.88-1.945.30.184109930.9660.0870.2043.65799.9
1.94-2.015.30.165109930.9690.0780.1844.56299.7
2.01-2.095.30.154109320.9710.0740.1725.18399.4
2.09-2.195.20.143109040.9710.0690.1596.22398.6
2.19-2.35.20.134107520.9720.0650.157.00797.4
2.3-2.445.20.125105970.9740.0610.147.35796.1
2.44-2.635.10.116103380.9760.0570.137.90593.1
2.63-2.94.90.199020.9810.050.1137.28989.3
2.9-3.324.70.07888030.9860.040.0886.36979
3.32-4.184.60.06267510.9920.0310.076.02960.3
4.18-504.60.05165670.9950.0250.0575.61157.1

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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: 1.541→39.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1696 / WRfactor Rwork: 0.1404 / FOM work R set: 0.9218 / SU B: 1.928 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0798 / SU Rfree: 0.0671 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1719 10324 5 %RANDOM
Rwork0.14 195983 --
obs0.1416 195983 92.96 %-
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: 75.16 Å2 / Biso mean: 21.072 Å2 / Biso min: 11.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0 Å2
2---0.17 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 1.541→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10366 0 26 1117 11509
Biso mean--30.72 28.64 -
Num. residues----1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910744
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210003
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.94614645
X-RAY DIFFRACTIONr_angle_other_deg0.812322950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54151323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03423.732544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.816151640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6871585
X-RAY DIFFRACTIONr_chiral_restr0.0840.21550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022641
X-RAY DIFFRACTIONr_rigid_bond_restr3.503320744
X-RAY DIFFRACTIONr_sphericity_free19.1985292
X-RAY DIFFRACTIONr_sphericity_bonded5.91521284
LS refinement shellResolution: 1.541→1.581 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 776 -
Rwork0.124 14543 -
all-15319 -
obs--94.2 %

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