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- PDB-2ebb: Crystal structure of pterin-4-alpha-carbinolamine dehydratase (pt... -

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Basic information

Entry
Database: PDB / ID: 2ebb
TitleCrystal structure of pterin-4-alpha-carbinolamine dehydratase (pterin carbinolamine dehydratase) from Geobacillus kaustophilus HTA426
ComponentsPterin-4-alpha-carbinolamine dehydratase
KeywordsLYASE / pterin-4-alpha-carbinolamine dehydratase / coenzyme biosyntheses / GK1984 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
4a-hydroxytetrahydrobiopterin dehydratase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of pterin-4-alpha-carbinolamine dehydratase (pterin carbinolamine dehydratase) from Geobacillus kaustophilus HTA426
Authors: Kumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S.
History
DepositionFeb 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pterin-4-alpha-carbinolamine dehydratase


Theoretical massNumber of molelcules
Total (without water)11,9851
Polymers11,9851
Non-polymers00
Water1,928107
1
A: Pterin-4-alpha-carbinolamine dehydratase

A: Pterin-4-alpha-carbinolamine dehydratase


Theoretical massNumber of molelcules
Total (without water)23,9692
Polymers23,9692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)46.866, 67.471, 31.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Pterin-4-alpha-carbinolamine dehydratase / Pterin carbinolamine dehydratase


Mass: 11984.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: GK1984 / Plasmid: pET-His TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codonplus-RIL-X
References: UniProt: Q5KYG7, 4a-hydroxytetrahydrobiopterin dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.6
Details: 30% MPD, 0.1M Actetate, 0.02M CaCl2, pH 4.6, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97915 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 20, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 13572 / Num. obs: 13572 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.135 / Num. unique all: 1275 / % possible all: 93.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 623847.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 677 5 %RANDOM
Rwork0.223 ---
obs0.223 13535 99.2 %-
all-13572 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3669 Å2 / ksol: 0.394974 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å20 Å20 Å2
2--1.4 Å20 Å2
3---0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 0 107 914
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 111 5.1 %
Rwork0.25 2062 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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