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- PDB-2qnk: Crystal structure of human 3-hydroxyanthranilate 3,4-dioxygenase -

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Basic information

Entry
Database: PDB / ID: 2qnk
TitleCrystal structure of human 3-hydroxyanthranilate 3,4-dioxygenase
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / Bicupin fold / cupin barrel / extradiol dioxygenase / metalloenzyme / trytophan catabolism / NAD+ synthesis / quinolinate / kynurenine pathway / Structural Genomics Medical Relevance / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


quinolinate metabolic process / 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / : / 'de novo' NAD+ biosynthetic process from L-tryptophan / quinolinate biosynthetic process / L-tryptophan catabolic process / Tryptophan catabolism / NAD+ biosynthetic process / neuron cellular homeostasis ...quinolinate metabolic process / 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / : / 'de novo' NAD+ biosynthetic process from L-tryptophan / quinolinate biosynthetic process / L-tryptophan catabolic process / Tryptophan catabolism / NAD+ biosynthetic process / neuron cellular homeostasis / response to zinc ion / response to cadmium ion / ferrous iron binding / electron transfer activity / cytosol / cytoplasm
Similarity search - Function
3-hydroxyanthranilate 3, 4-dioxygenase, metazoan / 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
NICKEL (II) ION / PHOSPHATE ION / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsBitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: to be published
Title: Crystal Structure of Human 3-hydroxyanthranilate 3,4-dioxygenase.
Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.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: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0323
Polymers32,8781
Non-polymers1542
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.498, 78.227, 85.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There is 1 biological unit in the asymmetric unit

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Components

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


Mass: 32878.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: HAAO / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) P(RARE2)
References: UniProt: P46952, 3-hydroxyanthranilate 3,4-dioxygenase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/ml Protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the well solution (50% v/v 2-Methyl-2,4- ...Details: Protein solution (10 mg/ml Protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the well solution (50% v/v 2-Methyl-2,4-pentanediol (MPD), 0.1 M PIPES pH 6.5) and cryoprotected with well solution, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97943, 0.96420
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2007 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979431
20.96421
ReflectionResolution: 1.6→37.4 Å / Num. obs: 45122 / % possible obs: 99.7 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.074 / Χ2: 1.238 / Net I/σ(I): 15.276
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.6-1.649.30.3774.103728601.0796.2
1.64-1.6810.70.3629291.0799.2
1.68-1.72120.29729641.07999.9
1.72-1.77130.26729821.143100
1.77-1.8313.90.23729821.204100
1.83-1.914.30.18829801.249100
1.9-1.9714.60.15229931.393100
1.97-2.0614.70.12629961.463100
2.06-2.1714.80.11130021.455100
2.17-2.3114.80.09330041.305100
2.31-2.4914.80.08429951.098100
2.49-2.7414.80.08330521.259100
2.74-3.1314.70.07330611.336100
3.13-3.9514.60.0530860.992100
3.95-37.413.90.04832361.28799.6

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Phasing

PhasingMethod: MAD
Phasing MAD set

Highest resolution: 1.6 Å / Lowest resolution: 32.53 Å

IDR cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_10000405504460
ISO_20.7440.7691.7451.289403714447
ANO_10.52702.3080402120
ANO_20.72800.9580401850
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_17-32.530000402217
ISO_15.01-70000776219
ISO_14.1-5.0100001032228
ISO_13.56-4.100001236215
ISO_13.19-3.5600001425230
ISO_12.91-3.1900001573223
ISO_12.7-2.9100001727221
ISO_12.53-2.700001860223
ISO_12.38-2.5300001982231
ISO_12.26-2.3800002117230
ISO_12.16-2.2600002211225
ISO_12.06-2.1600002324219
ISO_11.98-2.0600002436229
ISO_11.91-1.9800002526228
ISO_11.85-1.9100002627231
ISO_11.79-1.8500002725224
ISO_11.74-1.7900002783222
ISO_11.69-1.7400002887227
ISO_11.64-1.6900002963216
ISO_11.6-1.6400002938202
ANO_17-32.530.33203.61504010
ANO_15.01-70.33303.94807760
ANO_14.1-5.010.42502.965010320
ANO_13.56-4.10.42703.107012360
ANO_13.19-3.560.40603.195014250
ANO_12.91-3.190.37203.485015730
ANO_12.7-2.910.36803.65017270
ANO_12.53-2.70.38503.495018600
ANO_12.38-2.530.39903.252019820
ANO_12.26-2.380.43303.016021170
ANO_12.16-2.260.45302.727022110
ANO_12.06-2.160.46902.651023240
ANO_11.98-2.060.53202.283024360
ANO_11.91-1.980.59301.92025260
ANO_11.85-1.910.63601.769026270
ANO_11.79-1.850.71501.495027250
ANO_11.74-1.790.75701.314027830
ANO_11.69-1.740.81101.132028800
ANO_11.64-1.690.86101.018028880
ANO_11.6-1.640.8900.928026830
ISO_27-32.530.50.5862.8381.939402217
ISO_25.01-70.5620.672.7841.802776219
ISO_24.1-5.010.6920.8082.0531.371032228
ISO_23.56-4.10.7340.8331.9411.2241236215
ISO_23.19-3.560.7410.7421.9071.2861425230
ISO_22.91-3.190.7350.742.0181.361573223
ISO_22.7-2.910.7440.7712.1271.5151727221
ISO_22.53-2.70.7420.7822.1221.3421860223
ISO_22.38-2.530.7290.7652.0481.3391982231
ISO_22.26-2.380.7520.7241.9121.2932116230
ISO_22.16-2.260.7740.7991.8161.2442211225
ISO_22.06-2.160.7580.8021.7761.1092324219
ISO_21.98-2.060.7620.8151.6741.1082436229
ISO_21.91-1.980.7580.8131.5440.9912525228
ISO_21.85-1.910.7520.8541.4560.8922625231
ISO_21.79-1.850.7740.7811.3510.8322725224
ISO_21.74-1.790.7890.861.2070.7482782222
ISO_21.69-1.740.8050.9361.0680.6582882225
ISO_21.64-1.690.8290.9170.9040.5532938212
ISO_21.6-1.640.850.9160.7620.5722794195
ANO_27-32.530.53501.39804020
ANO_25.01-70.52101.54807760
ANO_24.1-5.010.56601.397010320
ANO_23.56-4.10.56201.491012360
ANO_23.19-3.560.55801.46014250
ANO_22.91-3.190.54501.499015730
ANO_22.7-2.910.55101.536017270
ANO_22.53-2.70.5701.479018600
ANO_22.38-2.530.60701.315019820
ANO_22.26-2.380.64601.24021160
ANO_22.16-2.260.68601.077022110
ANO_22.06-2.160.71301.008023240
ANO_21.98-2.060.75800.901024360
ANO_21.91-1.980.8200.778025250
ANO_21.85-1.910.8600.678026250
ANO_21.79-1.850.89300.588027250
ANO_21.74-1.790.91400.53027820
ANO_21.69-1.740.93900.451028720
ANO_21.64-1.690.95900.392028830
ANO_21.6-1.640.97100.37026730
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
112.2755.40952.096SE12.691.74
23.59548.31464.75SE14.751.26
37.5718.93966.774SE27.821.24
44.07919.33161.985SE14.541.05
511.31610.043.444SE27.671.14
611.56425.89320.334SE20.760.51
79.92954.59370.056SE12.790.54
81.30951.06184.287SE26.750.81
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 45010
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.46-10041.50.903514
5.65-7.4643.70.94623
4.74-5.6539.60.942759
4.16-4.7439.30.955867
3.75-4.1640.30.948972
3.44-3.7541.20.9521062
3.2-3.44400.9491125
3-3.240.60.9431199
2.84-338.30.9341289
2.7-2.84410.9351342
2.57-2.741.80.9321419
2.47-2.5742.20.9281470
2.37-2.4737.70.931517
2.29-2.3741.50.9211588
2.21-2.2943.50.9271641
2.14-2.2142.90.9221705
2.08-2.14440.9161736
2.02-2.0844.90.9141749
1.97-2.0244.90.9071842
1.92-1.9747.10.8991910
1.88-1.9248.80.8911914
1.83-1.8849.90.8791948
1.79-1.8352.10.8642009
1.76-1.7955.80.8592065
1.72-1.7656.30.8692105
1.69-1.7259.40.8552118
1.66-1.6962.40.8242166
1.63-1.6667.40.8052157
1.6-1.6365.50.7382199

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→30.92 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.163 / SU B: 2.49 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2268 5.036 %RANDOM
Rwork0.157 ---
obs0.158 45034 99.476 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--1.025 Å20 Å2
3----1.004 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 6 413 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222386
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9713240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03923.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88915415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8421521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021846
X-RAY DIFFRACTIONr_nbd_refined0.1990.21007
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.223
X-RAY DIFFRACTIONr_mcbond_it1.37821488
X-RAY DIFFRACTIONr_mcangle_it2.21942346
X-RAY DIFFRACTIONr_scbond_it3.58361021
X-RAY DIFFRACTIONr_scangle_it5.1168894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.6410.2861260.2422966328494.153
1.641-1.6850.2771830.2163012322399.131
1.685-1.7340.2321590.1912960312599.808
1.734-1.7870.1981470.1782865301499.934
1.787-1.8460.1961360.1692808294799.898
1.846-1.910.2021500.162719287199.93
1.91-1.9820.21420.1542609275299.964
1.982-2.0630.1561480.14825242672100
2.063-2.1540.1691200.14924272547100
2.154-2.2590.1641040.15123392443100
2.259-2.380.2061250.14822262351100
2.38-2.5230.193950.15421202215100
2.523-2.6960.1711140.16119672081100
2.696-2.9110.163910.15118561947100
2.911-3.1860.161010.151701180399.945
3.186-3.5570.134810.13215751656100
3.557-4.0980.159800.1313701450100
4.098-4.9970.126630.12712051268100
4.997-6.9770.192670.1939341001100
6.977-30.920.181360.22358362199.678
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)
10.6570.03670.51181.23940.99921.40990.0081-0.0020.1877-0.21950.0568-0.1121-0.22540.2866-0.0649-0.0955-0.02570.0156-0.0456-0.0037-0.073139.769165.889230.9319
20.97220.1565-0.54920.78370.11533.07650.04860.07690.1673-0.0720.00180.0939-0.3327-0.1529-0.0504-0.11840.01230.0093-0.14330.0031-0.128828.952567.093816.7434
30.35230.7891-1.30543.8352-3.60315.0601-0.01890.0436-0.0183-0.063-0.099-0.06670.05190.14030.1178-0.10820.02090.017-0.086-0.0119-0.093340.727364.22224.3275
41.59010.0039-2.18630.31460.86335.4048-0.02110.0378-0.1136-0.07080.03990.06610.2882-0.3329-0.0188-0.0991-0.04980.0061-0.05-0.0018-0.082521.701752.662428.2523
51.2852-0.3727-1.5891.39510.64034.7161-0.0501-0.199-0.1719-0.00880.014-0.12720.41960.13130.0361-0.136-0.00960.0019-0.10960.0166-0.100931.996551.977435.5161
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 361 - 36
2237 - 10437 - 104
33105 - 172105 - 172
44173 - 225173 - 225
55226 - 285226 - 285

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