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- PDB-4z6u: Structure of H200E variant of Homoprotocatechuate 2,3-Dioxygenase... -

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Basic information

Entry
Database: PDB / ID: 4z6u
TitleStructure of H200E variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-nitrocatechol at 1.48 Ang resolution
ComponentsHomoprotocatechuate 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / 2-His-1-carboxylate facial triad / oxygen activation / acid-base catalysis
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 ...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
4-NITROCATECHOL / : / Homoprotocatechuate 2,3-dioxygenase
Similarity search - Component
Biological speciesBrevibacterium fuscum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsKovaleva, E.G. / Lipscomb, J.D.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H001905/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 24689 United States
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200.
Authors: Kovaleva, E.G. / Rogers, M.S. / Lipscomb, J.D.
History
DepositionApr 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: 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 / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)168,95719
Polymers166,9854
Non-polymers1,97215
Water29,2201622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18100 Å2
ΔGint-137 kcal/mol
Surface area43720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.268, 150.875, 95.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

21D-913-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Homoprotocatechuate 2,3-dioxygenase


Mass: 41746.289 Da / Num. of mol.: 4 / Mutation: H200E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Plasmid: pYZW204 / Production host: Escherichia coli (E. coli) / Strain (production host): Jm109 / References: UniProt: Q45135

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Non-polymers , 6 types, 1637 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-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-4NC / 4-NITROCATECHOL


Mass: 155.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1622 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG6000, 0.1M calcium acetate, 0.1M MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.48→45.7 Å / Num. all: 262655 / Num. obs: 262655 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Rsym value: 0.061 / Net I/av σ(I): 10.703 / Net I/σ(I): 14.6 / Num. measured all: 1177706
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.48-1.564.40.8350.9169240381670.4250.835299.4
1.56-1.654.50.5371.5162943362330.2710.537399.6
1.65-1.774.50.3462.3153027340490.1750.3464.599.5
1.77-1.914.50.2073.8142423317590.1050.2077.199.5
1.91-2.094.50.1186.6131263291850.060.11811.999.3
2.09-2.344.50.07310.5119199264790.0370.07318.299.3
2.34-2.74.50.05114.6105799234120.0260.05124.299.2
2.7-3.314.50.0352088779197740.0180.03534.598.8
3.31-4.684.50.02427.768148152370.0120.02450.197.9
4.68-45.7064.40.02129.63688583600.0110.02151.695.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OJT

3ojt


Resolution: 1.48→45.7 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.1485 / WRfactor Rwork: 0.108 / FOM work R set: 0.8906 / SU B: 2.747 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0576 / SU Rfree: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 13081 5 %RANDOM
Rwork0.1174 ---
obs0.1196 249494 99.02 %-
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: 88.86 Å2 / Biso mean: 20.301 Å2 / Biso min: 8.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.48→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11510 0 115 1623 13248
Biso mean--29.85 32.68 -
Num. residues----1425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912201
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211125
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.94716584
X-RAY DIFFRACTIONr_angle_other_deg0.828325598
X-RAY DIFFRACTIONr_chiral_restr0.0970.21721
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023001
X-RAY DIFFRACTIONr_mcbond_it2.2581.7675856
X-RAY DIFFRACTIONr_mcbond_other2.2581.7665855
X-RAY DIFFRACTIONr_mcangle_it2.542.6557369
X-RAY DIFFRACTIONr_rigid_bond_restr3.296323326
X-RAY DIFFRACTIONr_sphericity_free30.0015441
X-RAY DIFFRACTIONr_sphericity_bonded10.921524192
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 964 -
Rwork0.232 18315 -
all-19279 -
obs--99.19 %

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