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- PDB-3n9t: Cryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 3n9t
TitleCryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomonas putida DLL-E4
ComponentsPnpC
KeywordsOXIDOREDUCTASE / PHOSPHOLIPID BINDS / N-TERMINAL HELIX TUNNEL
Function / homology
Function and homology information


catechol 1,2-dioxygenase activity / catechol-containing compound metabolic process / : / ferric iron binding
Similarity search - Function
Hydroxyquinol/catechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / Intradiol ring-cleavage dioxygenases signature. / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / CITRATE ANION / Chem-HGX / PnpC
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / ML / Resolution: 2 Å
AuthorsLiu, W. / Shen, W. / Fang, P. / Li, J. / Cui, Z.
CitationJournal: To be Published
Title: Cryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomonas putida DLL-E4
Authors: Liu, W. / Shen, W. / Fang, P. / Li, J. / Cui, Z.
History
DepositionMay 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: PnpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4414
Polymers32,4891
Non-polymers9523
Water1,874104
1
A: PnpC
hetero molecules

A: PnpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8828
Polymers64,9782
Non-polymers1,9046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6440 Å2
ΔGint-46 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.362, 38.933, 82.476
Angle α, β, γ (deg.)90.00, 118.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein PnpC / HYDROXYQUINOL 1 / 2-DIOXYGENASE


Mass: 32489.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: DLL-E4 / Gene: pnpC / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)) / References: UniProt: C6FI44, hydroxyquinol 1,2-dioxygenase
#2: Chemical ChemComp-HGX / 1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL CHOLINE


Mass: 706.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H77NO8P
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.33 Å3/Da / Density % sol: 47.31 % / Mosaicity: 0.552 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Hepes, trisodium citrate, pH 7.5, vapor diffusion, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.94722 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 29, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94722 Å / Relative weight: 1
ReflectionResolution: 2→72.58 Å / Num. obs: 20567 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.052 / Χ2: 0.96 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.244 / Num. unique all: 1024 / Χ2: 0.886 / % possible all: 99

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Phasing

PhasingMethod: ML
Phasing MRModel details: Phaser MODE: MR_FTF
Highest resolutionLowest resolution
Rotation2.5 Å36.29 Å
Translation2.5 Å36.29 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 20562
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.02-10033.20.734507
5.56-7.0238.60.854501
4.85-5.5629.20.908507
4.38-4.8527.80.934514
4.06-4.3828.20.932518
3.8-4.06310.91535
3.59-3.833.90.93568
3.41-3.5932.80.927618
3.25-3.4135.50.924634
3.11-3.2534.40.918684
2.99-3.1137.10.903669
2.88-2.9938.40.901735
2.79-2.8836.90.905735
2.7-2.79370.919764
2.62-2.736.90.903795
2.55-2.62370.896799
2.48-2.5537.10.903813
2.42-2.4840.70.912890
2.36-2.4242.20.899869
2.3-2.3642.30.903893
2.25-2.341.60.921915
2.21-2.25410.928937
2.16-2.2143.60.919959
2.12-2.1642.10.923970
2.08-2.12450.9191012
2.04-2.0846.80.903974
2-2.04520.8831247

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TMX

1tmx


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.839 / SU B: 3.965 / SU ML: 0.113 / SU R Cruickshank DPI: 0.186 / SU Rfree: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24384 1056 5.1 %RANDOM
Rwork0.18376 ---
obs0.18678 20562 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 23.531 Å2 / Biso min: 8.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.06 Å2
2--1.4 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 62 104 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222376
X-RAY DIFFRACTIONr_bond_other_d0.0030.025
X-RAY DIFFRACTIONr_angle_refined_deg1.911.9733215
X-RAY DIFFRACTIONr_angle_other_deg1.596311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5745285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26224.202119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30215356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.131515
X-RAY DIFFRACTIONr_chiral_restr0.1440.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211854
X-RAY DIFFRACTIONr_mcbond_it1.2941.51426
X-RAY DIFFRACTIONr_mcbond_other0.0271.52
X-RAY DIFFRACTIONr_mcangle_it2.2222300
X-RAY DIFFRACTIONr_scbond_it3.5253950
X-RAY DIFFRACTIONr_scangle_it5.1924.5915
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 87 -
Rwork0.198 1366 -
all-1453 -
obs--93.74 %

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