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- PDB-2o6i: Structure of an Enterococcus Faecalis HD Domain Phosphohydrolase -

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Basic information

Entry
Database: PDB / ID: 2o6i
TitleStructure of an Enterococcus Faecalis HD Domain Phosphohydrolase
ComponentsHD domain protein
KeywordsHYDROLASE / HD Domain / Phosphohydrolase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process / regulation of innate immune response / defense response to virus / nucleotide binding / metal ion binding
Similarity search - Function
HD-associated domain / Growth Hormone; Chain: A; - #30 / HD associated region / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / HD domain / Growth Hormone; Chain: A; / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain ...HD-associated domain / Growth Hormone; Chain: A; - #30 / HD associated region / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / HD domain / Growth Hormone; Chain: A; / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-HYDROXYETHYL DISULFIDE / HD domain protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.55 Å
AuthorsVorontsov, I.I. / Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Moy, S. / Collart, F.R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex.
Authors: Vorontsov, I.I. / Minasov, G. / Kiryukhina, O. / Brunzelle, J.S. / Shuvalova, L. / Anderson, W.F.
History
DepositionDec 7, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionDec 19, 2006ID: 2HON
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 23, 2011Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: HD domain protein
B: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1287
Polymers111,7722
Non-polymers3565
Water5,350297
1
A: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1414
Polymers55,8861
Non-polymers2553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9873
Polymers55,8861
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.913, 109.913, 182.412
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsChains A and B represent monomers of the protein

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Components

#1: Protein HD domain protein


Mass: 55886.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF-1143 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q836G9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M di-Sodium tartate dihydrate, 20 % w/v Polyethylene glycol 3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 19-ID21.0088
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDJan 31, 2006Mirrors
ADSC QUANTUM 3152CCDFeb 11, 2006Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 220 channelSINGLE WAVELENGTHMx-ray1
2Si 111 channelSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00881
ReflectionResolution: 2.55→30 Å / Num. all: 40637 / Num. obs: 40637 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3151 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.886 / SU B: 25.819 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31715 2049 5 %RANDOM
Rwork0.24845 ---
obs0.25179 38552 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 68.725 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å21.81 Å20 Å2
2--3.62 Å20 Å2
3----5.44 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7081 0 12 297 7390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0227436
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.94910089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9685892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.59523.514387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.153151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6661556
X-RAY DIFFRACTIONr_chiral_restr0.0880.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025761
X-RAY DIFFRACTIONr_nbd_refined0.2020.33707
X-RAY DIFFRACTIONr_nbtor_refined0.3180.55209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.5436
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.519
X-RAY DIFFRACTIONr_mcbond_it0.321.54556
X-RAY DIFFRACTIONr_mcangle_it0.57227197
X-RAY DIFFRACTIONr_scbond_it0.73533248
X-RAY DIFFRACTIONr_scangle_it1.2454.52892
LS refinement shellResolution: 2.551→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 113 -
Rwork0.298 2096 -
obs-2103 72.21 %
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)
11.64830.20720.22091.0753-0.21212.2078-0.0642-0.03030.17210.00190.06820.2436-0.378-0.3263-0.004-0.06630.08980.1075-0.36790.0088-0.1343-6.406921.388435.8336
21.46730.60160.43762.22450.55782.4031-0.11560.00140.3420.03340.1784-0.1058-0.85390.3494-0.06270.1769-0.15530.089-0.1129-0.0341-0.08263.891542.2534-3.3424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 45325 - 477
2X-RAY DIFFRACTION2BB-2 - 45322 - 477

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