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- PDB-4lrl: Structure of an Enterococcus Faecalis HD-domain protein complexed... -

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Basic information

Entry
Database: PDB / ID: 4lrl
TitleStructure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP
ComponentsHD domain protein
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / HD Domain / Phosphohydrolase / dNTPase / Allosteric Regulation / METAL BINDING PROTEIN
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 / MALONATE ION / NICKEL (II) ION / THYMIDINE-5'-TRIPHOSPHATE / HD domain protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVorontsov, I.I. / Minasov, G. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanisms of Allosteric Activation and Inhibition of the Deoxyribonucleoside Triphosphate Triphosphohydrolase from Enterococcus faecalis.
Authors: Vorontsov, I.I. / Wu, Y. / Delucia, M. / Minasov, G. / Mehrens, J. / Shuvalova, L. / Anderson, W.F. / Ahn, J.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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
C: HD domain protein
D: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,34219
Polymers223,5444
Non-polymers3,79815
Water13,223734
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20220 Å2
ΔGint-39 kcal/mol
Surface area68420 Å2
MethodPISA
2
A: HD domain protein
B: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,85411
Polymers111,7722
Non-polymers2,0829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-13 kcal/mol
Surface area37510 Å2
MethodPISA
3
C: HD domain protein
D: HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4888
Polymers111,7722
Non-polymers1,7166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-19 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.541, 144.625, 155.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsChains A, B, C and D form a tetramer

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Components

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Protein , 1 types, 4 molecules ABCD

#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 (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q836G9

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Non-polymers , 6 types, 749 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M MIB buffer (pH 5) and 25 % w/v PEG 1500, 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 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: Beryllium Lenses, Diamond [111] Laue monochromator
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 86389 / Num. obs: 86389 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 25.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8133 / % possible all: 94.9

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IRH

3irh


Resolution: 2.35→29.86 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.423 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23461 4304 5 %RANDOM
Rwork0.18437 ---
obs0.18693 81766 99.45 %-
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: 52.559 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2---0.82 Å2-0 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14717 0 224 734 15675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02215461
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.96821013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28551820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97523.524806
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.041152604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.98215114
X-RAY DIFFRACTIONr_chiral_restr0.0830.22251
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111897
X-RAY DIFFRACTIONr_mcbond_it0.41.59000
X-RAY DIFFRACTIONr_mcangle_it0.762214637
X-RAY DIFFRACTIONr_scbond_it1.21636461
X-RAY DIFFRACTIONr_scangle_it2.0154.56359
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 286 -
Rwork0.253 5677 -
obs--94.22 %
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)
11.8832-0.26360.39532.3987-0.43380.98760.0127-0.04-0.05790.1230.0152-0.03620.08630.1334-0.02780.0320.01390.00580.0299-0.01850.053745.6823.258835.5588
20.8808-0.2496-0.00453.7058-1.5211.74080.05230.27240.0467-0.01790.11920.0677-0.02720.0796-0.17150.07760.00340.00530.1594-0.04050.059843.89296.229718.9476
31.29140.36310.8161.19280.18144.3946-0.1240.52120.1351-0.28890.097-0.205-0.1510.37560.0270.1514-0.10470.05640.26930.07310.218149.864321.62589.545
43.84550.8380.93098.492-1.10212.13030.04520.6168-0.0565-0.7415-0.1811-0.7220.07140.54350.13590.24610.05680.00910.2256-0.06510.246746.4267-14.216318.2316
55.44783.8953-0.23797.21640.47819.0168-0.34910.79980.2729-0.76210.02990.172-0.3436-0.14610.31920.315-0.13780.0570.55540.00430.140442.649617.2051-7.525
62.03390.32680.56881.635-0.37681.2861-0.10420.12190.3443-0.1540.05050.3816-0.2227-0.24350.05370.14040.0424-0.04360.08420.02280.272319.305525.500217.2758
79.8431-0.3364-2.93654.29760.55351.4762-0.1993-0.5446-0.14980.23950.25540.36780.2261-0.3742-0.05610.1075-0.0799-0.09910.630.06750.41545.921814.585324.3949
81.13980.76631.03682.14380.57561.1265-0.0145-0.21310.21260.2449-0.08620.064-0.1989-0.1880.10070.21690.00350.03530.0499-0.04270.187234.100530.5841.4609
915.3563-8.10022.18293.9292-1.10610.06420.07391.43121.347-0.1371-0.6227-0.591-0.02320.17360.54880.852-0.14280.01091.1368-0.04952.115311.581928.30137.5013
1010.9917-1.32479.92732.9527-1.829814.3025-0.3897-0.6721.11590.4249-0.15810.2891-0.9752-0.36470.54780.2660.05430.10340.4658-0.07230.721-0.605119.340434.2015
1110.28072.30651.32037.07151.097414.6875-0.0041-0.8047-0.71311.3288-0.4118-0.00110.4313-0.35980.41580.5697-0.08860.08650.11960.01250.169233.389523.509960.5597
121.71330.11850.60121.5874-0.31162.31050.1421-0.2267-0.30590.2296-0.0552-0.0870.37530.0561-0.08690.1953-0.03890.00620.19950.02370.086412.7031-19.88541.0196
132.75520.20641.59390.4450.39812.2537-0.02730.02590.10310.1-0.0073-0.0232-0.11480.1660.03450.1278-0.03320.04830.20010.00030.05255.2724-5.030136.9757
143.1063-1.6936-0.05643.0439-0.10720.71490.0157-0.0094-0.26670.1069-0.02030.21010.2251-0.26180.00460.1162-0.12110.01780.2867-0.0020.1361-15.979-15.032326.9097
153.44014.66811.1537.83043.29183.51250.322-0.77570.45660.5539-0.5630.9826-0.0494-0.59060.2410.30110.08820.1910.95750.1880.25928.31582.042751.6613
169.1824-1.5371-0.62628.5019-0.5832.02010.10281.14810.5793-1.0987-0.0369-0.1409-0.18390.0746-0.06590.1893-0.0290.06740.35120.05660.313-20.6354.882920.6464
172.20670.96620.04261.6701-0.2882.7984-0.12490.3831-0.0165-0.27030.09890.04950.1045-0.10340.0260.1274-0.05850.00250.2461-0.02730.00586.0723-7.59214.3952
182.00570.5708-0.37413.1128-1.3872.0639-0.07220.2626-0.51570.01870.1675-0.03650.45190.15-0.09530.29060.0376-0.00240.2657-0.12040.158715.6684-20.71549.6645
193.9381-0.22961.7333.483-0.59464.54070.25980.0914-0.8777-0.00780.19670.06861.0884-0.1627-0.45650.5278-0.0922-0.05480.1477-0.06290.37353.288-33.533217.2444
203.15172.1462-0.16912.11930.72590.9447-0.53660.8076-0.9639-0.35510.5932-0.57450.29590.3616-0.05661.41390.37870.03321.1061-0.35351.468623.8029-35.45667.5245
213.53564.4866-3.4227.6208-5.24564.7942-0.32450.225-1.0124-0.9986-0.2106-0.70790.99350.80380.53510.62790.2413-0.11060.8347-0.35410.487529.5038-18.40424.9456
2232.912517.4982-0.67846.81240.49120.89630.88291.97782.00260.87661.38370.7240.98241.0834-2.26661.44621.2092-0.61141.5424-0.72754.089628.6918-48.619326.8179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 196
2X-RAY DIFFRACTION2A197 - 280
3X-RAY DIFFRACTION3A281 - 370
4X-RAY DIFFRACTION4A371 - 412
5X-RAY DIFFRACTION5A413 - 456
6X-RAY DIFFRACTION6B2 - 196
7X-RAY DIFFRACTION7B197 - 223
8X-RAY DIFFRACTION8B224 - 365
9X-RAY DIFFRACTION9B366 - 383
10X-RAY DIFFRACTION10B384 - 413
11X-RAY DIFFRACTION11B414 - 456
12X-RAY DIFFRACTION12C2 - 193
13X-RAY DIFFRACTION13C194 - 267
14X-RAY DIFFRACTION14C268 - 370
15X-RAY DIFFRACTION15C371 - 412
16X-RAY DIFFRACTION16C413 - 456
17X-RAY DIFFRACTION17D1 - 195
18X-RAY DIFFRACTION18D196 - 284
19X-RAY DIFFRACTION19D285 - 332
20X-RAY DIFFRACTION20D333 - 383
21X-RAY DIFFRACTION21D384 - 426
22X-RAY DIFFRACTION22D435 - 447

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