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

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Basic information

Entry
Database: PDB / ID: 4ghd
TitleStructure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with HPCA at 1.85 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
2-(3,4-DIHYDROXYPHENYL)ACETIC ACID / : / Homoprotocatechuate 2,3-dioxygenase
Similarity search - Component
Biological speciesBrevibacterium fuscum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)169,49021
Polymers166,9574
Non-polymers2,53217
Water21,7081205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-40 kcal/mol
Surface area44600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.163, 150.701, 96.107
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 , 7 types, 1222 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-DHY / 2-(3,4-DIHYDROXYPHENYL)ACETIC ACID


Mass: 168.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1205 / 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: 48.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM HPCA for 3 hours in anaerobic glovebox atmosphere prior to cryo-cooling in liquid nitrogen., ...Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM HPCA for 3 hours in anaerobic glovebox atmosphere prior to cryo-cooling in liquid nitrogen., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 21, 2011
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.85→48.1 Å / Num. all: 134568 / Num. obs: 134568 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.9 / Num. unique all: 19149 / % possible all: 97.3

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Processing

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

3ojt


Resolution: 1.85→48.05 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.194 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18899 6740 5 %RANDOM
Rwork0.15187 ---
obs0.15374 127788 98.44 %-
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: 27.973 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11566 0 154 1205 12925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212305
X-RAY DIFFRACTIONr_bond_other_d0.0010.028429
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.94516703
X-RAY DIFFRACTIONr_angle_other_deg0.93320332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08951492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94123.472671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.942151942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.97715110
X-RAY DIFFRACTIONr_chiral_restr0.0980.21726
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022714
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 426 -
Rwork0.256 8747 -
obs--95.94 %
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)
10.7491-0.27480.12110.6459-0.09890.2187-0.00530.15910.3124-0.0708-0.0856-0.1954-0.05640.05010.09090.0593-0.005-0.00460.05410.0940.171912.113453.11376.1975
20.4892-0.0691-0.09660.30530.05270.35040.01320.20710.0119-0.0791-0.0283-0.06660.0089-0.10010.01510.06780.00330.02310.14950.02710.031112.239322.3382-7.4366
30.5502-0.0576-0.03520.52880.02510.5088-0.022-0.10050.08750.14880.00260.013-0.028-0.0630.01950.08250.01160.00230.0473-0.00880.0248-2.51730.749838.9382
40.65440.03360.08570.67940.04470.41380.0081-0.0391-0.06740.1393-0.0071-0.16610.08170.056-0.0010.07350.0132-0.03950.02280.01680.068724.699412.279231.0005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 358
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B3 - 362
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C2 - 357
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION4D3 - 362
8X-RAY DIFFRACTION4D401

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