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- PDB-4z6v: Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase... -

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Basic information

Entry
Database: PDB / ID: 4z6v
TitleStructure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-nitrocatechol at 1.37 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: 1.37 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_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)168,91818
Polymers166,9814
Non-polymers1,93714
Water34,9491940
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18030 Å2
ΔGint-125 kcal/mol
Surface area43740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.180, 150.635, 96.103
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-626-

HOH

21D-968-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Homoprotocatechuate 2,3-dioxygenase


Mass: 41745.305 Da / Num. of mol.: 4 / Mutation: H200Q
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, 1954 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.: 3 / 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.: 1940 / 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: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 14% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.37→45.691 Å / Num. all: 325847 / Num. obs: 325847 / % possible obs: 97.9 % / Redundancy: 4.1 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.073 / Rsym value: 0.064 / Net I/av σ(I): 10.779 / Net I/σ(I): 14.2 / Num. measured all: 1340516
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
1.37-1.444.10.7861189430462530.4320.7861.995.9
1.44-1.534.10.4911.6182274442740.270.491396.9
1.53-1.644.10.3082.6173592419760.170.3084.797.6
1.64-1.774.20.24163160393140.110.26.998.2
1.77-1.944.20.126.6151278364060.0660.1210.898.6
1.94-2.174.10.07111137063330340.0390.07117.798.7
2.17-2.54.10.04915.5120914293160.0270.04924.599
2.5-3.064.10.03620.1102178249700.020.03632.199.3
3.06-4.3340.02526.978320194930.0140.02546.699.4
4.33-45.6913.90.02130.142307108110.0120.02149.298

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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: 1.37→40.35 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.1415 / WRfactor Rwork: 0.1067 / FOM work R set: 0.9016 / SU B: 2.023 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0455 / SU Rfree: 0.0465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1567 16249 5 %RANDOM
Rwork0.1187 ---
obs0.1206 309539 97.69 %-
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: 79.5 Å2 / Biso mean: 16.321 Å2 / Biso min: 6.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.37→40.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11519 0 114 1955 13588
Biso mean--24.24 30.12 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211110
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.94716537
X-RAY DIFFRACTIONr_angle_other_deg0.803325559
X-RAY DIFFRACTIONr_chiral_restr0.0870.21716
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022995
X-RAY DIFFRACTIONr_mcbond_it1.5191.3735840
X-RAY DIFFRACTIONr_mcbond_other1.5171.3725839
X-RAY DIFFRACTIONr_mcangle_it1.8062.0677342
X-RAY DIFFRACTIONr_rigid_bond_restr1.975323283
X-RAY DIFFRACTIONr_sphericity_free32.2755498
X-RAY DIFFRACTIONr_sphericity_bonded10.129524427
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 1168 -
Rwork0.255 22175 -
all-23343 -
obs--95.38 %

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