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- PDB-3eck: Structure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevi... -

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Basic information

Entry
Database: PDB / ID: 3eck
TitleStructure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrations
ComponentsPROTEIN (Homoprotocatechuate 2,3-dioxygenase)
KeywordsOXIDOREDUCTASE / oxygenase / extradiol / FeII / crystal packing / Dioxygenase
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
homoprotocatechuate 2,3-dioxygenase fold / homoprotocatechuate 2,3-dioxygenase domains / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, Mn/Fe-type / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, C-terminal domain superfamily / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. ...homoprotocatechuate 2,3-dioxygenase fold / homoprotocatechuate 2,3-dioxygenase domains / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, Mn/Fe-type / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, C-terminal domain superfamily / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Few Secondary Structures / Irregular / Roll / Alpha Beta
Similarity search - Domain/homology
: / Chem-XXG / Homoprotocatechuate 2,3-dioxygenase
Similarity search - Component
Biological speciesBrevibacterium fuscum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKovaleva, E.G. / Lipscomb, J.D.
CitationJournal: Biochemistry / Year: 2008
Title: Intermediate in the O-O Bond Cleavage Reaction of an Extradiol Dioxygenase.
Authors: Kovaleva, E.G. / Lipscomb, J.D.
History
DepositionAug 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (Homoprotocatechuate 2,3-dioxygenase)
B: PROTEIN (Homoprotocatechuate 2,3-dioxygenase)
C: PROTEIN (Homoprotocatechuate 2,3-dioxygenase)
D: PROTEIN (Homoprotocatechuate 2,3-dioxygenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,32821
Polymers166,9574
Non-polymers1,37017
Water25,0951393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16760 Å2
ΔGint-105 kcal/mol
Surface area43620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.735, 163.176, 101.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PROTEIN (Homoprotocatechuate 2,3-dioxygenase)


Mass: 41739.363 Da / Num. of mol.: 4 / Mutation: E323L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Strain: ATCC 15993 / Gene: hpcd / Plasmid: pYZW204 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase

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Non-polymers , 6 types, 1410 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-XXG / 3,3-dihydroxy-4-oxocyclohexa-1,5-diene-1-sulfonic acid / 1,1-dihydroxy-2-keto-5-sulfonyl-cyclohexa-3,5-diene


Mass: 206.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O6S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1393 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG8000, 0.1M Ca acetate, 0.1M Na cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.6→55 Å / Num. all: 240583 / Num. obs: 222399 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 19.22
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.067 / Num. unique all: 17442 / % possible all: 73.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2IG9

2ig9


Resolution: 1.6→24.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.553 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19767 11135 5 %RANDOM
Rwork0.17401 ---
obs0.17521 211226 92.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.045 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11596 0 71 1393 13060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02112264
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.94716720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70451518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27723.463667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.249151961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.86615108
X-RAY DIFFRACTIONr_chiral_restr0.0950.21753
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029764
X-RAY DIFFRACTIONr_nbd_refined0.20.25983
X-RAY DIFFRACTIONr_nbtor_refined0.3040.28397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.21360
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.220
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0970.22
X-RAY DIFFRACTIONr_mcbond_it0.71.57501
X-RAY DIFFRACTIONr_mcangle_it1.078211870
X-RAY DIFFRACTIONr_scbond_it1.76935371
X-RAY DIFFRACTIONr_scangle_it2.7154.54825
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 598 -
Rwork0.292 11609 -
obs--69.64 %

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