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- PDB-3zds: Structure of homogentisate 1,2-dioxygenase in complex with reacti... -

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Basic information

Entry
Database: PDB / ID: 3zds
TitleStructure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of homogentisate with oxygen.
ComponentsHOMOGENTISATE 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / EXTRADIOL / ALKYLPEROXO SPECIES / HOMOGENTISATE-SEMIQUINONE / RING-FISSION PRODUCT
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 / cytoplasm
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
: / Chem-HMQ / Chem-HQ9 / 4-Maleylacetoacetic acid / 2-(3,6-DIHYDROXYPHENYL)ACETIC ACID / OXYGEN MOLECULE / PHOSPHATE ION / Homogentisate 1,2-dioxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJeoung, J.-H. / Bommer, M. / Lin, T.-Y. / Dobbek, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Visualizing the Substrate-, Superoxo-, Alkylperoxo- and Product-Bound States at the Non-Heme Fe(II) Site of Homogentisate Dioxygenase
Authors: Jeoung, J.-H. / Bommer, M. / Lin, T.-Y. / Dobbek, H.
History
DepositionNov 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Atomic model / Derived calculations / Other
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / reflns_shell / 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 / _reflns_shell.Rmerge_I_obs / _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

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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)579,63638
Polymers576,72512
Non-polymers2,91126
Water102,7045701
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
G: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,86520
Polymers288,3636
Non-polymers1,50314
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
J: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

F: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

L: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

H: HOMOGENTISATE 1,2-DIOXYGENASE
I: HOMOGENTISATE 1,2-DIOXYGENASE
K: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,77018
Polymers288,3636
Non-polymers1,40812
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_654x+1,y,z-11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_644x+1,y-1,z-11
identity operation1_555x,y,z1
MethodPISA
3
J: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

F: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

L: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

H: HOMOGENTISATE 1,2-DIOXYGENASE
I: HOMOGENTISATE 1,2-DIOXYGENASE
K: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,77018
Polymers288,3636
Non-polymers1,40812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_456x-1,y,z+11
MethodPISA
4
F: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

J: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

L: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

H: HOMOGENTISATE 1,2-DIOXYGENASE
I: HOMOGENTISATE 1,2-DIOXYGENASE
K: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,77018
Polymers288,3636
Non-polymers1,40812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_645x+1,y-1,z1
crystal symmetry operation1_556x,y,z+11
MethodPISA
5
L: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

F: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

J: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules

H: HOMOGENTISATE 1,2-DIOXYGENASE
I: HOMOGENTISATE 1,2-DIOXYGENASE
K: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,77018
Polymers288,3636
Non-polymers1,40812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_466x-1,y+1,z+11
MethodPISA
Unit cell
Length a, b, c (Å)93.737, 93.857, 163.438
Angle α, β, γ (deg.)87.62, 80.39, 68.29
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#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: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88E47, homogentisate 1,2-dioxygenase

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Non-polymers , 8 types, 5727 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-M8O / 4-Maleylacetoacetic acid


Mass: 200.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O6
#4: Chemical
ChemComp-OMD / 2-(3,6-DIHYDROXYPHENYL)ACETIC ACID / HOMOGENTISIC ACID


Mass: 168.147 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H8O4
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-HQ9 / 2-(6-oxidanyl-3-oxidanylidene-cyclohexa-1,4-dien-1-yl)ethanoic acid


Mass: 168.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O4
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-HMQ / 2-[(6R)-6-(dioxidanyl)-6-oxidanyl-3-oxidanylidene-cyclohexa-1,4-dien-1-yl]ethanoic acid


Mass: 200.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O6
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5701 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details2,5-DIHYDROXYPHENYLACETIC ACID (HQ9): 1 ELECTRON OXIDIZED 2,5-DIHYDROXYPHENYL-DIOXO ACETIC ACID ...2,5-DIHYDROXYPHENYLACETIC ACID (HQ9): 1 ELECTRON OXIDIZED 2,5-DIHYDROXYPHENYL-DIOXO ACETIC ACID (HMQ): FORMED COVALENT BOND WITH DIOXYGEN

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion
Details: VAPOUR DIFFUSION (1:1 MIX): 17% PEG 3350, 0.02 M NAK PHOSPHATE AND 0.1 M BIS-TRIS PROPANE PH 8.0, 1MM TCEP, 2 MICROM HOMOGENTISATE, 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: 1.7→35 Å / Num. obs: 532721 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 16.64 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.85
Reflection shellResolution: 1.7→35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.13 / % possible all: 91.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EYB

1eyb


Resolution: 1.7→34.37 Å / Cor.coef. Fo:Fc: 0.9002 / Cor.coef. Fo:Fc free: 0.8608 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 26681 5.01 %RANDOM
Rwork0.2031 ---
obs0.2055 532705 94.91 %-
Displacement parametersBiso mean: 18.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.8778 Å2-1.1551 Å21.0538 Å2
2--1.7939 Å2-0.0271 Å2
3----2.6717 Å2
Refine analyzeLuzzati coordinate error obs: 0.223 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39964 0 169 5701 45834
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0141635HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1956807HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d13832SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes968HARMONIC2
X-RAY DIFFRACTIONt_gen_planes6226HARMONIC5
X-RAY DIFFRACTIONt_it41635HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion18.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5143SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact52536SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2663 1910 5.04 %
Rwork0.2179 35998 -
all0.2204 37908 -
obs--94.91 %
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)
10.30190.09110.00360.1960.01090.23640.015-0.0833-0.05260.0742-0.0279-0.03530.06890.03950.0129-0.01-0.01030.0006-0.05150.0229-0.10261.131234.50670.2267
20.3847-0.0896-0.04740.3373-0.01190.22870.0168-0.06510.0620.0618-0.013-0.0159-0.07760.059-0.0038-0.028-0.0445-0.0009-0.0781-0.0152-0.0867.841873.2007-5.7591
30.18370.0431-0.04340.2519-0.10610.26690.0104-0.00840.06720.05150.00150.0916-0.04-0.0869-0.0119-0.0673-0.00670.0318-0.0583-0.0102-0.0624-29.174758.5565-8.7585
40.3506-0.00120.01410.2166-0.04440.1869-0.02530.0626-0.0655-0.04530.01370.02030.0749-0.05370.0116-0.0258-0.03680.0173-0.0617-0.0059-0.0906-14.282529.988-40.2433
50.33070.0529-0.04040.1599-0.01050.1823-0.00810.09980.1013-0.05720.02580.0633-0.0579-0.055-0.0177-0.0306-0.0111-0.0063-0.05340.0413-0.0868-10.71569.0317-46.8491
60.350.0593-0.08390.25790.00440.1354-0.01260.08780.0609-0.07930.0080.0652-0.0527-0.0610.0047-0.10060.0122-0.00790.03270.0266-0.1126.095724.863734.0737
70.26860.0735-0.01660.3381-0.02150.2708-0.01940.0195-0.0286-0.03480.0142-0.07960.02760.07640.0052-0.0646-0.01020.0313-0.04610.0063-0.083921.561247.5971-38.0378
80.36370.0546-0.09380.28590.03880.2280.0334-0.09670.11420.053-0.0138-0.0021-0.07620.0313-0.0196-0.102-0.01330.01740.0223-0.04-0.114618.323841.2228-88.4488
90.31240.1125-0.08520.4306-0.08070.21780.0058-0.0681-0.01350.0651-0.0060.12670.0311-0.05180.0002-0.134-0.00460.03410.0343-0.0038-0.0824-11.167314.6168-87.0231
100.358-0.0167-0.03330.46360.05750.1691-0.010.0512-0.019-0.05370.0093-0.0603-0.0160.05470.0007-0.1225-0.00640.0290.02840.0064-0.1023-29.2116.454939.9605
110.34540.1366-0.04930.3240.05650.09760.0065-0.1682-0.12890.1106-0.0215-0.08080.05850.07190.015-0.10190.0159-0.00270.06190.0699-0.117526.37012.9228-80.7076
120.1972-0.03-0.06220.24510.01060.2105-0.02090.0487-0.1596-0.0410.00040.00140.0853-0.03520.0205-0.1116-0.0140.0293-0.0252-0.0178-0.054-21.44574.690341.9471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

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