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- PDB-4aq2: resting state of homogentisate 1,2-dioxygenase -

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Basic information

Entry
Database: PDB / ID: 4aq2
Titleresting state of homogentisate 1,2-dioxygenase
ComponentsHOMOGENTISATE 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


homogentisate 1,2-dioxygenase / homogentisate 1,2-dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / iron ion binding / negative regulation of DNA-templated transcription
Similarity search - Function
Homogentisate 1,2-dioxygenase, bacterial / Homogentisate 1,2-dioxygenase / Homogentisate 1,2-dioxygenase, C-terminal domain / Homogentisate 1,2-dioxygenase, N-terminal domain / Homogentisate 1,2-dioxygenase C-terminal / Homogentisate 1,2-dioxygenase N-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls ...Homogentisate 1,2-dioxygenase, bacterial / Homogentisate 1,2-dioxygenase / Homogentisate 1,2-dioxygenase, C-terminal domain / Homogentisate 1,2-dioxygenase, N-terminal domain / Homogentisate 1,2-dioxygenase C-terminal / Homogentisate 1,2-dioxygenase N-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Homogentisate 1,2-dioxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJeoung, J.-H. / Lin, T.-Y. / Bommer, M. / Dobbek, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Visualizing the Substrate-, Superoxo-, Alkylperoxo-, and Product-Bound States at the Nonheme Fe(II) Site of Homogentisate Dioxygenase.
Authors: Jeoung, J.-H. / Bommer, M. / Lin, T.-Y. / Dobbek, H.
History
DepositionApr 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Other
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.status_code_sf / _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: HOMOGENTISATE 1,2-DIOXYGENASE
B: HOMOGENTISATE 1,2-DIOXYGENASE
C: HOMOGENTISATE 1,2-DIOXYGENASE
D: HOMOGENTISATE 1,2-DIOXYGENASE
E: HOMOGENTISATE 1,2-DIOXYGENASE
F: HOMOGENTISATE 1,2-DIOXYGENASE
G: HOMOGENTISATE 1,2-DIOXYGENASE
H: HOMOGENTISATE 1,2-DIOXYGENASE
I: HOMOGENTISATE 1,2-DIOXYGENASE
J: HOMOGENTISATE 1,2-DIOXYGENASE
K: HOMOGENTISATE 1,2-DIOXYGENASE
L: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)577,67825
Polymers576,72512
Non-polymers95213
Water102,2535676
1
A: HOMOGENTISATE 1,2-DIOXYGENASE
B: HOMOGENTISATE 1,2-DIOXYGENASE
C: HOMOGENTISATE 1,2-DIOXYGENASE
D: HOMOGENTISATE 1,2-DIOXYGENASE
E: HOMOGENTISATE 1,2-DIOXYGENASE
F: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,69812
Polymers288,3636
Non-polymers3356
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44200 Å2
ΔGint-275.5 kcal/mol
Surface area76670 Å2
MethodPISA
2
G: HOMOGENTISATE 1,2-DIOXYGENASE
H: HOMOGENTISATE 1,2-DIOXYGENASE
I: HOMOGENTISATE 1,2-DIOXYGENASE
J: HOMOGENTISATE 1,2-DIOXYGENASE
K: HOMOGENTISATE 1,2-DIOXYGENASE
L: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,98013
Polymers288,3636
Non-polymers6177
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43910 Å2
ΔGint-273.2 kcal/mol
Surface area76830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.737, 93.901, 162.810
Angle α, β, γ (deg.)87.46, 80.45, 68.33
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 9:433 )
211CHAIN B AND (RESSEQ 9:433 )
311CHAIN C AND (RESSEQ 9:433 )
411CHAIN D AND (RESSEQ 9:433 )
511CHAIN E AND (RESSEQ 9:433 )
611CHAIN F AND (RESSEQ 9:433 )
711CHAIN G AND (RESSEQ 9:433 )
811CHAIN H AND (RESSEQ 9:433 )
911CHAIN I AND (RESSEQ 9:433 )
1011CHAIN J AND (RESSEQ 9:433 )
1111CHAIN K AND (RESSEQ 9:433 )
1211CHAIN L AND (RESSEQ 9:433 )

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Components

#1: Protein
HOMOGENTISATE 1,2-DIOXYGENASE / / HOMOGENTISATE OXYGENASE / HOMOGENTISIC ACID OXIDASE / HOMOGENTISICASE


Mass: 48060.422 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: KT2440 / Description: DSM / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q88E47, homogentisate 1,2-dioxygenase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5676 / 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: 2.28 Å3/Da / Density % sol: 45.98 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 8
Details: VAPOUR DIFFUSION(1:1): 17 % PEG 3350, 0.02 M NAK PHOSPHATE, 0.1 M BIS-TRIS PROPANE PH 8.0, 1 MM TCEP 15 MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→34 Å / Num. obs: 359608 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 16.33 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.38 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EYB

1eyb


Resolution: 1.95→33.936 Å / SU ML: 0.64 / σ(F): 1.99 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 17580 5 %
Rwork0.1925 --
obs0.1958 351605 94.82 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.245 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.431 Å20.5355 Å20.7097 Å2
2--1.5511 Å20.0005 Å2
3---1.2577 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39464 0 31 5676 45171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941226
X-RAY DIFFRACTIONf_angle_d1.10956342
X-RAY DIFFRACTIONf_dihedral_angle_d14.05315234
X-RAY DIFFRACTIONf_chiral_restr0.0765876
X-RAY DIFFRACTIONf_plane_restr0.0057546
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3293X-RAY DIFFRACTIONPOSITIONAL
12B3293X-RAY DIFFRACTIONPOSITIONAL0.046
13C3241X-RAY DIFFRACTIONPOSITIONAL0.049
14D3276X-RAY DIFFRACTIONPOSITIONAL0.049
15E3278X-RAY DIFFRACTIONPOSITIONAL0.051
16F3246X-RAY DIFFRACTIONPOSITIONAL0.047
17G3252X-RAY DIFFRACTIONPOSITIONAL0.047
18H3255X-RAY DIFFRACTIONPOSITIONAL0.047
19I3278X-RAY DIFFRACTIONPOSITIONAL0.048
110J3276X-RAY DIFFRACTIONPOSITIONAL0.045
111K3331X-RAY DIFFRACTIONPOSITIONAL0.046
112L3260X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01970.319315500.229929444X-RAY DIFFRACTION84
2.0197-2.10050.299517720.212733672X-RAY DIFFRACTION95
2.1005-2.19610.289917820.200733854X-RAY DIFFRACTION96
2.1961-2.31190.284717590.197233425X-RAY DIFFRACTION95
2.3119-2.45670.286317950.19334114X-RAY DIFFRACTION97
2.4567-2.64630.270417910.187534026X-RAY DIFFRACTION97
2.6463-2.91250.26818000.190534201X-RAY DIFFRACTION97
2.9125-3.33360.244817940.186834078X-RAY DIFFRACTION97
3.3336-4.19880.227417770.18233767X-RAY DIFFRACTION96
4.1988-33.94090.220817600.189633444X-RAY DIFFRACTION95

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