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- PDB-4ghf: Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase... -

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Basic information

Entry
Database: PDB / ID: 4ghf
TitleStructure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution
ComponentsHomoprotocatechuate 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / oxygen activation / Fe(II) / 2-His-1-carboxylate facial triad / homoprotocatechuate / 4-nitrocatechol / oxy complex
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 / : / OXYGEN MOLECULE / Homoprotocatechuate 2,3-dioxygenase
Similarity search - Component
Biological speciesBrevibacterium fuscum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsKovaleva, E.G. / Lipscomb, J.D.
CitationJournal: Biochemistry / Year: 2012
Title: Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation.
Authors: Kovaleva, E.G. / Lipscomb, J.D.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Sep 13, 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 / 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_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.ptnr2_auth_asym_id / _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.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.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.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

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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)169,69225
Polymers166,9574
Non-polymers2,73521
Water21,0601169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14010 Å2
ΔGint-36 kcal/mol
Surface area44570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.519, 150.318, 96.105
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
Homoprotocatechuate 2,3-dioxygenase


Mass: 41739.320 Da / Num. of mol.: 4 / Mutation: Y257F
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): JM109
References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase

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Non-polymers , 8 types, 1190 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-4NC / 4-NITROCATECHOL


Mass: 155.108 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5NO4
#4: 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
#5: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1169 / 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: 48.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM 4-nitrocatechol under aerobic conditions for 1hr prior to cryo-cooling in liquid nitrogen. , ...Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM 4-nitrocatechol under aerobic conditions for 1hr prior to cryo-cooling in liquid nitrogen. , pH pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.67→96.11 Å / Num. all: 184533 / Num. obs: 184533 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.5
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
REFMAC5.6.0117phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OJT

3ojt


Resolution: 1.67→89.04 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.567 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18052 9169 5 %RANDOM
Rwork0.15087 ---
obs0.15236 175300 99.53 %-
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 mean: 27.656 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.67→89.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11508 0 167 1169 12844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212260
X-RAY DIFFRACTIONr_bond_other_d0.0010.028370
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9516648
X-RAY DIFFRACTIONr_angle_other_deg0.955320199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08351486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72223.483666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.741151932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.59815108
X-RAY DIFFRACTIONr_chiral_restr0.1110.21719
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022709
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 659 -
Rwork0.251 12299 -
obs--99.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.779-0.35940.20280.5997-0.0960.2424-0.00990.16460.3448-0.0703-0.0971-0.2071-0.05360.0620.10710.0752-0.008-0.00240.0620.09490.206212.231652.98756.1504
20.559-0.0203-0.22240.33090.05560.3778-0.01370.22890.0125-0.07980.0099-0.06220.0092-0.14240.00380.0768-0.01160.01690.17430.02180.020812.312322.2363-7.3382
30.60310.027-0.00610.56560.1010.5186-0.0016-0.11740.1130.1245-0.02160.027-0.0089-0.0550.02320.07390.0090.00520.0728-0.02070.0261-2.579330.526538.9352
40.67110.0970.11910.63420.07050.38020.0137-0.0617-0.08940.11690.0032-0.14810.0720.0372-0.01680.06830.0178-0.02680.04060.01140.059424.78412.360731.1105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 358
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B4 - 362
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C4 - 354
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION4D4 - 362
8X-RAY DIFFRACTION4D401

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