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- PDB-4hsl: 2.00 angstrom x-ray crystal structure of substrate-bound E110A 3-... -

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Entry
Database: PDB / ID: 4hsl
Title2.00 angstrom x-ray crystal structure of substrate-bound E110A 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans
Components3-hydroxyanthranilate 3,4-dioxygenaseHAAO
KeywordsOXIDOREDUCTASE / bi-cupin iron-binding / dioxygenase
Function / homology
Function and homology information


3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / quinolinate biosynthetic process / anthranilate metabolic process / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / ferrous iron binding
Similarity search - Function
3-hydroxyanthranilic acid dioxygenase / 3-hydroxyanthranilic acid dioxygenase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
3-HYDROXYANTHRANILIC ACID / : / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, F. / Chen, L. / Liu, A.
CitationJournal: To be Published
Title: 2.00 angstrom x-ray crystal structure of substrate-bound E110A 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans
Authors: Liu, F. / Chen, L. / Liu, A.
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2634
Polymers19,9991
Non-polymers2653
Water25214
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5278
Polymers39,9972
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area4400 Å2
ΔGint-47 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.461, 58.461, 232.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 3-hydroxyanthranilate 3,4-dioxygenase / HAAO / 3-hydroxyanthranilate oxygenase / 3-HAO / 3-hydroxyanthranilic acid dioxygenase / HAD


Mass: 19998.600 Da / Num. of mol.: 1 / Mutation: E110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: Cupriavidus metallidurans, nbaC, Rmet_5193 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DH5 alpha)
References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-3HA / 3-HYDROXYANTHRANILIC ACID / 2-AMINO-3-HYDROXYBENZOIC ACID / 3-Hydroxyanthranilic acid


Mass: 153.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 8000, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 16978 / Num. obs: 14975 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.2 % / Rsym value: 0.095 / Net I/σ(I): 58.72
Reflection shellResolution: 2→2.03 Å / % possible all: 42.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YFY

1yfy


Resolution: 2→21.19 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.42 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 730 4.9 %RANDOM
Rwork0.2232 ---
all0.2256 16907 --
obs0.2256 14873 87.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.7 Å2 / Biso mean: 49.9975 Å2 / Biso min: 26.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å21.26 Å20 Å2
2--1.26 Å20 Å2
3----4.07 Å2
Refinement stepCycle: LAST / Resolution: 2→21.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 13 14 1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191463
X-RAY DIFFRACTIONr_bond_other_d0.0020.021329
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9451993
X-RAY DIFFRACTIONr_angle_other_deg0.9333048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9765173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97922.69278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48115215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0191514
X-RAY DIFFRACTIONr_chiral_restr0.120.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 27 -
Rwork0.3 504 -
all-531 -
obs--44.03 %

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