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- PDB-1b4u: PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATE... -

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Basic information

Entry
Database: PDB / ID: 1b4u
TitlePROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)
Components(PROTOCATECHUATE 4,5-DIOXYGENASE) x 2
KeywordsDIOXYGENASE / EXTRADIOL TYPE DIOXYGENASE / PROTOCATECHUATE / NON-HEME IRON PROTEIN
Function / homology
Function and homology information


protocatechuate 4,5-dioxygenase / protocatechuate 4,5-dioxygenase activity / : / 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 / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Dioxygenase LigAB, LigA subunit superfamily / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B ...Protocatechuate 4,5-dioxygenase, alpha subunit / Protocatechuate 4,5-dioxygenase beta chain / Protocatechuate 4,5-dioxygenase; Chain A / Dioxygenase LigAB, LigA subunit / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Dioxygenase LigAB, LigA subunit superfamily / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3,4-DIHYDROXYBENZOIC ACID / : / 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. / Mitsui, Y.
CitationJournal: Structure Fold.Des. / 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
DepositionDec 29, 1998Processing site: BNL
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / pdbx_struct_conn_angle / 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 / _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.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_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: PROTOCATECHUATE 4,5-DIOXYGENASE
B: PROTOCATECHUATE 4,5-DIOXYGENASE
C: PROTOCATECHUATE 4,5-DIOXYGENASE
D: PROTOCATECHUATE 4,5-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2018
Polymers97,7814
Non-polymers4204
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-91 kcal/mol
Surface area29840 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:
IDCodeMatrixVector
1given(-0.472399, -0.858231, -0.200693), (-0.855572, 0.391816, 0.338343), (-0.211742, 0.33154, -0.919373)124.29021, 65.23419, 45.96177
2given(-0.491695, -0.847546, -0.199753), (-0.847604, 0.413294, 0.332799), (-0.199505, 0.332947, -0.921599)124.6075, 63.82454, 45.3572

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Components

#1: Protein PROTOCATECHUATE 4,5-DIOXYGENASE / LIGA / LIGB


Mass: 15567.516 Da / Num. of mol.: 2 / Fragment: CHAIN A, C, ALPHA CHAIN, CHAIN B, D, BETA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK-6 / Production host: Escherichia coli (E. coli)
References: UniProt: P22635, protocatechuate 4,5-dioxygenase
#2: Protein PROTOCATECHUATE 4,5-DIOXYGENASE / LIGA / LIGB


Mass: 33322.996 Da / Num. of mol.: 2 / Fragment: CHAIN A, C, ALPHA CHAIN, CHAIN B, D, BETA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK-6 / 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: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 53.76 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal
*PLUS
Density % sol: 53.4 %
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: Jul 29, 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: 45587 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11
Reflection
*PLUS
Num. measured all: 91377

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→60 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.22 -10 %RANDOM
Rwork0.161 ---
obs-45584 91 %-
Refinement stepCycle: LAST / Resolution: 2.2→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6684 0 24 189 6897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.161 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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