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- PDB-5bwh: Structure of H200C variant of Homoprotocatechuate 2,3-Dioxygenase... -

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Basic information

Entry
Database: PDB / ID: 5bwh
TitleStructure of H200C variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with HPCA at 1.46 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
2-(3,4-DIHYDROXYPHENYL)ACETIC ACID / : / Homoprotocatechuate 2,3-dioxygenase
Similarity search - Component
Biological speciesBrevibacterium fuscum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 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: Inorg.Chem. / Year: 2015
Title: A Long-Lived Fe(III)-(Hydroperoxo) Intermediate in the Active H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Characterization by Mossbauer, Electron Paramagnetic Resonance, and Density ...Title: A Long-Lived Fe(III)-(Hydroperoxo) Intermediate in the Active H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Characterization by Mossbauer, Electron Paramagnetic Resonance, and Density Functional Theory Methods.
Authors: Meier, K.K. / Rogers, M.S. / Kovaleva, E.G. / Mbughuni, M.M. / Bominaar, E.L. / Lipscomb, J.D. / Munck, E.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.3Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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_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_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.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)168,96418
Polymers166,8814
Non-polymers2,08214
Water27,0591502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14600 Å2
ΔGint-48 kcal/mol
Surface area44240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.414, 151.027, 96.468
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-583-

HOH

21D-865-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Homoprotocatechuate 2,3-dioxygenase


Mass: 41720.316 Da / Num. of mol.: 4 / Mutation: H200C
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, 1516 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.: 2 / 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-DHY / 2-(3,4-DIHYDROXYPHENYL)ACETIC ACID


Mass: 168.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O4 / Comment: neurotransmitter*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1502 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 13-15% PEG6K, 0.1M calcium chloride, 0.1M MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.46→29.7 Å / Num. all: 269165 / Num. obs: 269165 / % possible obs: 96.9 % / Redundancy: 3.8 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.068 / Rsym value: 0.059 / Net I/av σ(I): 8.76 / Net I/σ(I): 12.3 / Num. measured all: 1025435
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
1.46-1.543.80.712144592377920.4090.71294
1.54-1.633.80.4531.7140399367150.260.4533.196.2
1.63-1.753.90.2922.6133545345300.1660.2924.696.4
1.75-1.883.90.1774.3125800325530.1010.177797.3
1.88-2.063.80.1067.2113092299160.0610.10611.197.2
2.06-2.313.90.06910.7106155273740.0390.06916.498.1
2.31-2.673.70.05113.790937243370.030.05120.698.3
2.67-3.263.80.0416.178333206480.0230.0427.298.5
3.26-4.623.70.0321959433161550.0190.03234.898.7
4.62-29.6563.60.02919.43314991450.0180.02935.298.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OJT

3ojt


Resolution: 1.46→29.66 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.1556 / WRfactor Rwork: 0.117 / FOM work R set: 0.8969 / SU B: 2.504 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0578 / SU Rfree: 0.0553 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 13391 5 %RANDOM
Rwork0.1217 ---
obs0.1236 255730 96.69 %-
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: 105.55 Å2 / Biso mean: 20.44 Å2 / Biso min: 9.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.46→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11555 0 126 1506 13187
Biso mean--28.78 31.27 -
Num. residues----1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912290
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211217
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.94716703
X-RAY DIFFRACTIONr_angle_other_deg0.789325802
X-RAY DIFFRACTIONr_chiral_restr0.0870.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023027
X-RAY DIFFRACTIONr_mcbond_it1.9042.45900
X-RAY DIFFRACTIONr_mcbond_other1.8982.45899
X-RAY DIFFRACTIONr_mcangle_it2.174.0567431
X-RAY DIFFRACTIONr_rigid_bond_restr2.408323507
X-RAY DIFFRACTIONr_sphericity_free25.7465394
X-RAY DIFFRACTIONr_sphericity_bonded9.969524295
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 919 -
Rwork0.248 17763 -
all-18682 -
obs--91.68 %

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