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- PDB-2v6t: Crystal structure of a complex of pterin-4a-carbinolamine dehydra... -

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Basic information

Entry
Database: PDB / ID: 2v6t
TitleCrystal structure of a complex of pterin-4a-carbinolamine dehydratase from Toxoplasma gondii with 7,8-dihydrobiopterin
ComponentsPTERIN-4A-CARBINOLAMINE DEHYDRATASE
KeywordsLYASE / PTERIN / ENZYME / TAUTOMER / TOXOPLASMA / DEHYDRATASE
Function / homology
Function and homology information


4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / tetrahydrobiopterin biosynthetic process
Similarity search - Function
Transcriptional coactivator/pterin dehydratase / Pterin 4 alpha carbinolamine dehydratase / Pterin 4 alpha carbinolamine dehydratase superfamily / Pterin 4 alpha carbinolamine dehydratase / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H2B / 4a-hydroxytetrahydrobiopterin dehydratase
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCameron, S. / Fyffe, S.A. / Hunter, W.N.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2008
Title: Crystal Structures of Toxoplasma Gondii Pterin-4A-Carbinolamine Dehydratase and Comparisons with Mammalian and Parasite Orthologues.
Authors: Cameron, S. / Fyffe, S.A. / Goldie, S. / Hunter, W.N.
History
DepositionJul 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim
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 / _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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
B: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7764
Polymers24,2972
Non-polymers4782
Water19811
1
A: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
B: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
hetero molecules

A: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
B: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5528
Polymers48,5954
Non-polymers9574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7100 Å2
ΔGint-48.7 kcal/mol
Surface area21940 Å2
MethodPQS
Unit cell
Length a, b, c (Å)119.510, 119.510, 49.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12A
22B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLUGLU2BB5 - 1037 - 105
21ALAALAGLUGLU2AA5 - 1037 - 105
12H2BH2BH2BH2B1AC1104
22H2BH2BH2BH2B1BD1104

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.09057, -0.9245, 0.3704), (-0.9258, -0.05892, -0.3734), (0.3671, -0.3767, -0.8505)
Vector: -67.18, 62.33, -23.38)

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Components

#1: Protein PTERIN-4A-CARBINOLAMINE DEHYDRATASE


Mass: 12148.687 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: MODIFIED PET15B (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2Q449, 4a-hydroxytetrahydrobiopterin dehydratase
#2: Chemical ChemComp-H2B / 2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE / QUINONOID 7,8-TETRAHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGH AT N-TERMINUS IS LEFT WHEN HEXAHIS TAG IS REMOVED

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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: 3.82 Å3/Da / Density % sol: 67.6 % / Description: NONE
Crystal growpH: 7.6 / Details: 0.4 M POTASSIUM-SODIUM TARTRATE, pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 7, 2006 / Details: OSMIC CONFOCAL OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→43 Å / Num. obs: 6969 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6S

2v6s


Resolution: 3.1→42.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.873 / SU B: 18.034 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 341 4.9 %RANDOM
Rwork0.187 ---
obs0.19 6591 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 3.1→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 34 11 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211701
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2541.9262309
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4365197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7724.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.20715267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6158
X-RAY DIFFRACTIONr_chiral_restr0.1430.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021325
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2860.2792
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21160
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8111.51004
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59221578
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2833803
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6174.5731
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B392tight positional0.10.05
21A17tight positional0.040.05
22B17tight positional0.040.05
11B404medium positional0.440.5
11B392tight thermal0.360.5
21A17tight thermal0.310.5
22B17tight thermal0.310.5
11B404medium thermal0.992
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 24
Rwork0.285 470

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