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- PDB-1ru0: Crystal structure of DCoH2, a paralog of DCoH, the Dimerization C... -

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Basic information

Entry
Database: PDB / ID: 1ru0
TitleCrystal structure of DCoH2, a paralog of DCoH, the Dimerization Cofactor of HNF-1
ComponentsDcoH-like protein DCoHm
KeywordsLYASE / alpha and beta structure
Function / homology
Function and homology information


4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / phenylalanine 4-monooxygenase activity / tetrahydrobiopterin biosynthetic process / mitochondrion / identical protein binding / nucleus
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
Pterin-4-alpha-carbinolamine dehydratase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRose, R.B. / Pullen, K.E. / Bayle, J.H. / Crabtree, G.R. / Alber, T.
Citation
Journal: Biochemistry / Year: 2004
Title: Biochemical and structural basis for partially redundant enzymatic and transcriptional functions of DCoH and DCoH2
Authors: Rose, R.B. / Pullen, K.E. / Bayle, J.H. / Crabtree, G.R. / Alber, T.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha
Authors: Rose, R.B. / Bayle, J.H. / Endrizzi, J.A. / Cronk, J.D. / Crabtree, G.R. / Alber, T.
History
DepositionDec 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DcoH-like protein DCoHm
B: DcoH-like protein DCoHm


Theoretical massNumber of molelcules
Total (without water)23,7992
Polymers23,7992
Non-polymers00
Water2,936163
1
A: DcoH-like protein DCoHm
B: DcoH-like protein DCoHm

A: DcoH-like protein DCoHm
B: DcoH-like protein DCoHm


Theoretical massNumber of molelcules
Total (without water)47,5984
Polymers47,5984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)58.290, 58.290, 114.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-180-

HOH

21B-164-

HOH

DetailsA dimer is in the asymmetric unit, which interacts with HNF-1. DCoH2 is a tetramer in solution. The tetramer is generated by rotating the dimer around the crystallographic two-fold axis: -x, -x+y, -z+1/3.

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Components

#1: Protein DcoH-like protein DCoHm


Mass: 11899.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: DCOHM / Organ: liver / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9CZL5, 4a-hydroxytetrahydrobiopterin dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: isopropanol, PEG 4000, Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2000
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 30110 / Num. obs: 30110 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.066 / Net I/σ(I): 12.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 4325 / Rsym value: 0.253 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DCO

1dco


Resolution: 1.6→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1508 -random
Rwork0.212 ---
all0.213 30087 --
obs0.213 30087 99.9 %-
Solvent computationBsol: 89.3426 Å2 / ksol: 0.414439 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.265 Å2-1.004 Å20 Å2
2---2.265 Å20 Å2
3---4.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 0 163 1718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.19
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection
Rfree0.2449 127
Rwork0.2643 -
obs-2491
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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