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- PDB-1q0c: Anerobic Substrate Complex of Homoprotocatechuate 2,3-Dioxygenase... -

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Basic information

Entry
Database: PDB / ID: 1q0c
TitleAnerobic Substrate Complex of Homoprotocatechuate 2,3-Dioxygenase from Brevibacterium fuscum. (Complex with 3,4-Dihydroxyphenylacetate)
Componentshomoprotocatechuate 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Extradiol Dioxygenase / Substrate Complex
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
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 ...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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVetting, M.W. / Wackett, L.P. / Que, L. / Lipscomb, J.D. / Ohlendorf, D.H.
CitationJournal: J.Bacteriol. / Year: 2004
Title: Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.
Authors: Vetting, M.W. / Wackett, L.P. / Que, L. / Lipscomb, J.D. / Ohlendorf, D.H.
History
DepositionJul 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5May 2, 2018Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_label_seq_id / _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)167,91712
Polymers167,0214
Non-polymers8968
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13870 Å2
ΔGint-86 kcal/mol
Surface area40850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.0, 157.0, 122.3
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsCrystal contains a tetramer per assymetric unit. Biologically active protein exists as a tetramer.

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Components

#1: Protein
homoprotocatechuate 2,3-dioxygenase / 3 / 4-dihydroxyphenylacetate 2 / 3-dioxygenase


Mass: 41755.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-DHY / 2-(3,4-DIHYDROXYPHENYL)ACETIC ACID


Mass: 168.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H8O4 / Comment: neurotransmitter*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 291 K / Method: batch / pH: 7.5
Details: 10% Peg5000 MME, 0.2 M Magnesium Acetate, 100 mM Mops, pH 7.5, batch, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 1999
RadiationMonochromator: CuK(alpha) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 82936 / Num. obs: 82936 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.19 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.2 / Num. unique all: 8482 / Rsym value: 0.216 / % possible all: 99.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 4152 -random
Rwork0.17 ---
all-82929 --
obs-82929 96 %-
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10404 0 52 373 10829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.91
X-RAY DIFFRACTIONc_bond_d0.016

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