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- PDB-1bou: THREE-DIMENSIONAL STRUCTURE OF LIGAB -

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Basic information

Entry
Database: PDB / ID: 1bou
TitleTHREE-DIMENSIONAL STRUCTURE OF LIGAB
Components
  • 4,5-DIOXYGENASE ALPHA CHAIN
  • 4,5-DIOXYGENASE BETA CHAIN
KeywordsDIOXYGENASE / EXTRADIOL TYPE DIOXYGENASE / OXIDOREDUCTASE
Function / homology
Function and homology information


protocatechuate 4,5-dioxygenase / protocatechuate 4,5-dioxygenase activity / catabolic process / ferrous iron binding
Similarity search - Function
Protocatechuate 4,5-dioxygenase, alpha subunit / Protocatechuate 4,5-dioxygenase beta chain / Protocatechuate 4,5-dioxygenase; Chain A / Dioxygenase LigAB, LigA subunit / Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase ...Protocatechuate 4,5-dioxygenase, alpha subunit / Protocatechuate 4,5-dioxygenase beta chain / Protocatechuate 4,5-dioxygenase; Chain A / Dioxygenase LigAB, LigA subunit / Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / Dioxygenase LigAB, LigA subunit superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Protocatechuate 4,5-dioxygenase alpha chain / Protocatechuate 4,5-dioxygenase beta chain
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.2 Å
AuthorsSugimoto, K. / Senda, T. / Fukuda, M. / Mitsui, Y.
CitationJournal: Structure / Year: 1999
Title: Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.
Authors: Sugimoto, K. / Senda, T. / Aoshima, H. / Masai, E. / Fukuda, M. / Mitsui, Y.
History
DepositionAug 6, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Assembly

Deposited unit
A: 4,5-DIOXYGENASE ALPHA CHAIN
B: 4,5-DIOXYGENASE BETA CHAIN
C: 4,5-DIOXYGENASE ALPHA CHAIN
D: 4,5-DIOXYGENASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8936
Polymers97,7814
Non-polymers1122
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-93 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.400, 66.500, 119.800
Angle α, β, γ (deg.)90.00, 92.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.481, -0.853, -0.203), (-0.854, 0.404, 0.329), (-0.199, 0.332, -0.922)
Vector: 124.614, 64.942, 45.412)

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Components

#1: Protein 4,5-DIOXYGENASE ALPHA CHAIN / LIGA


Mass: 15567.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK6 / Production host: Escherichia coli (E. coli)
References: UniProt: P22635, protocatechuate 4,5-dioxygenase
#2: Protein 4,5-DIOXYGENASE BETA CHAIN / LIGB


Mass: 33322.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK6 / Production host: Escherichia coli (E. coli)
References: UniProt: P22636, protocatechuate 4,5-dioxygenase
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.66 Å3/Da / Density % sol: 53.4 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Sugimoto, K., (1999) Protein Peptide Lett., 6, 55.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
137.0 mg/mlprotein1drop
2100 mMTris-HCl1drop
350 %satammonium sulfate1reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 9, 1998 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. obs: 43335 / % possible obs: 86.5 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 2.9 / % possible all: 58
Reflection
*PLUS
Num. measured all: 80490

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
PROCESSdata reduction
PROCESSdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→60 Å / Rfactor Rfree error: 0.0031 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4363 10 %RANDOM
Rwork0.149 ---
obs0.149 43335 86.5 %-
Refinement stepCycle: LAST / Resolution: 2.2→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6686 0 2 200 6888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.228 409 10 %
Rwork0.208 3694 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 43259 / Rfactor obs: 0.16 / Rfactor Rfree: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67

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