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- PDB-2ch1: Structure of Anopheles gambiae 3-hydroxykynurenine transaminase -

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Basic information

Entry
Database: PDB / ID: 2ch1
TitleStructure of Anopheles gambiae 3-hydroxykynurenine transaminase
Components3-HYDROXYKYNURENINE TRANSAMINASE
KeywordsTRANSFERASE / PLP-ENZYME / KYNURENINE PATHWAY / ANOPHELES GAMBIAE / 3-HYDROXYKYNURENINE TRANSAMINASE
Function / homology
Function and homology information


alanine-glyoxylate transaminase / L-kynurenine catabolic process / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / glycine biosynthetic process, by transamination of glyoxylate / L-serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / pyridoxal phosphate binding / peroxisome
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 3-hydroxykynurenine transaminase / 3-hydroxykynurenine transaminase
Similarity search - Component
Biological speciesANOPHELES GAMBIAE (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRossi, F. / Garavaglia, S. / Giovenzana, G.B. / Arca, B. / Li, J. / Rizzi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Crystal Structure of the Anopheles Gambiae 3-Hydroxykynurenine Transaminase
Authors: Rossi, F. / Garavaglia, S. / Giovenzana, G.B. / Arca, B. / Li, J. / Rizzi, M.
History
DepositionMar 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: 3-HYDROXYKYNURENINE TRANSAMINASE
B: 3-HYDROXYKYNURENINE TRANSAMINASE
C: 3-HYDROXYKYNURENINE TRANSAMINASE
D: 3-HYDROXYKYNURENINE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,75712
Polymers177,4004
Non-polymers1,3578
Water6,269348
1
A: 3-HYDROXYKYNURENINE TRANSAMINASE
D: 3-HYDROXYKYNURENINE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3796
Polymers88,7002
Non-polymers6784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-42.4 kcal/mol
Surface area26890 Å2
MethodPISA
2
B: 3-HYDROXYKYNURENINE TRANSAMINASE
C: 3-HYDROXYKYNURENINE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3796
Polymers88,7002
Non-polymers6784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-41.3 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.434, 84.167, 118.793
Angle α, β, γ (deg.)90.00, 99.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 2 - 389 / Label seq-ID: 2 - 389

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
3-HYDROXYKYNURENINE TRANSAMINASE


Mass: 44350.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANOPHELES GAMBIAE (African malaria mosquito)
Strain: GASUA / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4LAM2, UniProt: Q7PRG3*PLUS
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.43 Å3/Da / Density % sol: 50 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 65686 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 3.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0C

1h0c


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.038 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1 AND 390-396 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND NOT INCLUDED IN THE FINAL MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.246 986 1.5 %RANDOM
Rwork0.213 ---
obs0.213 64670 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.83 Å2
2--2.35 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12175 0 84 348 12607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212544
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.97317005
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1551548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34223.502534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.464152135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3931584
X-RAY DIFFRACTIONr_chiral_restr0.1020.21852
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029454
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.26196
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.28515
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4240.2130
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7591.57940
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.195212449
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88335294
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0064.54556
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3033 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.060.05
3Ctight positional0.060.05
4Dtight positional0.060.05
1Atight thermal0.150.5
2Btight thermal0.180.5
3Ctight thermal0.180.5
4Dtight thermal0.20.5
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 68
Rwork0.287 4785

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