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- PDB-3irh: Structure of an Enterococcus Faecalis HD-domain protein complexed... -

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Basic information

Entry
Database: PDB / ID: 3irh
TitleStructure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP
ComponentsHD domain protein
KeywordsHYDROLASE / HD Domain / Phosphohydrolase / dNTPase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / unknown function
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process / nucleotide binding / metal ion binding
Similarity search - Function
Growth Hormone; Chain: A; - #30 / HD-associated domain / HD associated region / Hypothetical protein af1432 / Hypothetical protein af1432 / : / HD domain / HD domain / Growth Hormone; Chain: A; / Metal dependent phosphohydrolases with conserved 'HD' motif. ...Growth Hormone; Chain: A; - #30 / HD-associated domain / 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'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / HD domain protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVorontsov, I.I. / Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / 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
DepositionAug 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: HD domain protein
B: HD domain protein
C: HD domain protein
D: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,71514
Polymers223,5444
Non-polymers3,17110
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4333
Polymers55,8861
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9244
Polymers55,8861
Non-polymers1,0383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4333
Polymers55,8861
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9244
Polymers55,8861
Non-polymers1,0383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.253, 188.660, 67.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsauthors state that chains A, B, C and D form a tetramer

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Components

#1: Protein
HD domain protein


Mass: 55886.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF-1143, EF_1143 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q836G9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 295 K / pH: 7.5
Details: 0.2 M Sodium bromide, 0.1 M Bis-tris propane pH 7.5, 20 % w/v Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 18, 2008 / Details: BERYLLIUM LENSES/DIAMOND LAUE MONO
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 75951 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2O6I

2o6i


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.65 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.567 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3783 5 %RANDOM
Rwork0.185 ---
obs0.188 71324 99.2 %-
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: 40.67 Å2
Baniso -1Baniso -2Baniso -3
1--5.12 Å20 Å20 Å2
2--2.09 Å20 Å2
3---3.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14635 0 188 409 15232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02215352
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.96720854
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49351804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70323.468793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.873152602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.62715116
X-RAY DIFFRACTIONr_chiral_restr0.0860.22238
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.27067
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.210578
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2741
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2450.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6931.59189
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.211214606
X-RAY DIFFRACTIONr_scbond_it1.90736952
X-RAY DIFFRACTIONr_scangle_it3.064.56247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 256 -
Rwork0.233 4979 -
obs--95.32 %
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)
12.0343-0.0480.10031.23890.0021.2939-0.06120.03930.0494-0.0607-0.0160.17930.0429-0.18530.07720.0238-0.0315-0.0188-0.0523-0.0285-0.236-73.23931.003-17.498
22.0473-0.43940.10791.60010.01690.5989-0.03360.2937-0.3469-0.27080.0393-0.15170.18040.0675-0.00570.123-0.02740.0283-0.0265-0.0984-0.1752-52.51819.461-26.821
36.2489-1.6761.56855.3857-2.38911.7234-0.03870.77170.0214-0.83740.13590.32220.2599-0.1286-0.09720.2481-0.0671-0.06260.2107-0.0071-0.1686-68.17141.654-37.483
47.9271-4.1889-0.989112.9191-1.74677.3992-0.0379-0.1847-0.0043-0.42550.335-1.2642-0.09520.5027-0.29710.2233-0.06860.17870.0652-0.19060.0034-33.21423.332-35.264
51.26250.10290.03841.402-0.10750.9487-0.0172-0.0651-0.04760.1032-0.0294-0.15530.07260.00710.0465-0.00760.0292-0.0171-0.12470.0326-0.2313-39.27234.32-0.688
64.0305-0.3614-1.81761.51830.33941.8524-0.1189-0.479-0.49410.091-0.0554-0.11280.18570.06150.17440.0715-0.00780.0107-0.03150.0992-0.1112-61.71612.9247.353
715.58062.9739-1.30473.3759-0.06557.07820.167-0.8783-1.52020.5561-0.2629-0.42660.8582-0.06440.09590.27740.0237-0.07620.03590.0258-0.0636-42.92546.23617.582
811.5111-0.6869-0.02363.95881.16826.76170.4393-0.10990.0095-0.0219-0.49670.5879-0.5852-0.60790.05740.13760.04240.01540.0957-0.0783-0.1408-79.75321.87115.545
92.6766-0.2777-0.23832.0729-0.13261.16990.04730.0245-0.1596-0.0572-0.07550.4387-0.0484-0.08890.0282-0.02730.0229-0.0138-0.1293-0.0322-0.1609-72.17666.949-4.606
101.9340.15690.22921.3030.26420.5481-0.048-0.18470.22150.15520.0441-0.0175-0.14340.09690.00390.04020.0130.0117-0.0805-0.0361-0.1916-50.08678.7954.74
117.55932.6541-2.10287.7786-3.27242.13180.1355-0.4455-0.06831.16670.06840.5172-0.317-0.1187-0.20390.28070.03590.07010.23120.0513-0.0531-66.16156.89115.182
1210.63840.28271.76298.5506-3.3526.42360.11060.17460.0982-0.0536-0.1893-1.0730.37420.75730.07870.06710.0716-0.0590.0306-0.1186-0.0894-29.59573.99513.726
131.2441-0.3224-0.24921.28210.2741.21510.01570.1106-0.0262-0.146-0.0349-0.0695-0.06680.06440.01910.0062-0.0117-0.0003-0.10590.0184-0.2632-36.91163.573-20.226
141.719-0.8543-0.11321.7520.6480.74480.12390.35740.3604-0.4361-0.2898-0.0087-0.298-0.19990.16590.22260.06-0.03730.05490.1073-0.1691-58.15379.411-29.514
1519.7005-4.57173.8525.46060.61366.90820.24780.77941.5177-0.4278-0.3624-0.5748-0.6760.32580.11460.2238-0.02090.10180.04690.0717-0.1671-41.950.72-40.098
164.9998-4.06380.67513.6986-0.53629.83520.2339-0.0464-0.4512-0.2204-0.40441.27350.0919-1.28130.17060.30540.0718-0.1860.34-0.14370.0309-76.54976.016-36.983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 209
2X-RAY DIFFRACTION2A210 - 366
3X-RAY DIFFRACTION3A367 - 410
4X-RAY DIFFRACTION4A411 - 456
5X-RAY DIFFRACTION5B1 - 244
6X-RAY DIFFRACTION6B245 - 371
7X-RAY DIFFRACTION7B383 - 411
8X-RAY DIFFRACTION8B412 - 456
9X-RAY DIFFRACTION9C1 - 213
10X-RAY DIFFRACTION10C214 - 366
11X-RAY DIFFRACTION11C367 - 415
12X-RAY DIFFRACTION12C416 - 456
13X-RAY DIFFRACTION13D1 - 218
14X-RAY DIFFRACTION14D219 - 369
15X-RAY DIFFRACTION15D384 - 410
16X-RAY DIFFRACTION16D411 - 456

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