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- PDB-2yeu: Structural and functional insights of DR2231 protein, the MazG-li... -

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Basic information

Entry
Database: PDB / ID: 2yeu
TitleStructural and functional insights of DR2231 protein, the MazG-like nucleoside triphosphate pyrophosphohydrolase from Deinococcus radiodurans, complex with Gd
ComponentsDR2231
KeywordsHYDROLASE / DIMERIC DUTPASE
Function / homology
Function and homology information


nucleoside triphosphate diphosphatase activity / metal ion binding
Similarity search - Function
putative ntp pyrophosphohydrolase like fold / putative ntp pyrophosphohydrolase like domain / NTP pyrophosphohydrolase-like domain superfamily / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GADOLINIUM ATOM / HAD superfamily Cof-like phosphohydrolase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGoncalves, A.M.D. / de Sanctis, D. / McSweeney, S.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans.
Authors: Goncalves, A.M.D. / Desanctis, D. / Mcsweeney, S.M.
History
DepositionMar 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references / Non-polymer description / Version format compliance
Revision 2.0Nov 20, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_conn.ptnr2_label_seq_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: DR2231
B: DR2231
C: DR2231
D: DR2231
E: DR2231
F: DR2231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,66749
Polymers100,2526
Non-polymers4,41443
Water12,286682
1
A: DR2231
B: DR2231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,04118
Polymers33,4172
Non-polymers1,62416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-141.6 kcal/mol
Surface area16180 Å2
MethodPISA
2
C: DR2231
D: DR2231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,85716
Polymers33,4172
Non-polymers1,43914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-132.9 kcal/mol
Surface area16290 Å2
MethodPISA
3
E: DR2231
F: DR2231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,76915
Polymers33,4172
Non-polymers1,35113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-113.6 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.820, 110.750, 165.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DR2231


Mass: 16708.691 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9RS96, nucleoside-triphosphate diphosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Gd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.05 % / Description: NONE
Crystal growDetails: 0.01M MAGNESIUM CHLORIDE, 0.05M SODIUM CACODYLATE PH6.0, 1M LITHIUM SULPHATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.24
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2009 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2→83 Å / Num. obs: 85194 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→92.06 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.917 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 4090 5 %RANDOM
Rwork0.18787 ---
obs0.19008 77944 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→92.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6814 0 212 682 7708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0217138
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5262.0049692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8835879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8323.174334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.191151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4861578
X-RAY DIFFRACTIONr_chiral_restr0.1040.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0225464
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8151.54460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41927120
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4432678
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8724.52572
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 264 -
Rwork0.237 5316 -
obs--89.73 %
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)
10.41290.0012-0.01550.4770.12351.07630.0061-0.0034-0.0733-0.0057-0.03250.01630.082-0.05210.02650.0152-0.00270.00690.0517-0.01580.055418.281234.825715.1312
20.242-0.1911-0.35380.870.50591.9706-0.02760.01310.0405-0.0131-0.04370.1223-0.1045-0.24160.07130.02480.0079-0.01540.0534-0.02290.052116.038539.56813.6972
30.80390.0297-0.16210.5417-0.09311.20720.00520.0052-0.0707-0.0075-0.02240.03140.0959-0.07230.01730.01540.00020.00730.01070.0030.046745.886221.173940.7905
40.9276-0.1245-0.13560.66010.11871.03690.02240.0154-0.012-0.0114-0.0295-0.10450.0330.12040.00710.01110.0050.00580.02130.01620.042851.059721.51641.7581
50.2842-0.1363-0.5770.74520.13172.3802-0.0612-0.1087-0.05940.2061-0.0594-0.04160.160.27070.12060.1177-0.01520.03090.08440.01090.089514.892841.32170.1561
60.53320.20310.0211.28880.42861.24240.0446-0.1521-0.13390.4356-0.12430.05550.3370.05430.07970.1887-0.03330.05230.10240.00890.090611.726937.10368.4118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 22
2X-RAY DIFFRACTION1A23 - 144
3X-RAY DIFFRACTION2B-5 - 28
4X-RAY DIFFRACTION2B29 - 144
5X-RAY DIFFRACTION3C-4 - 22
6X-RAY DIFFRACTION3C23 - 144
7X-RAY DIFFRACTION4D-5 - 24
8X-RAY DIFFRACTION4D25 - 144
9X-RAY DIFFRACTION5E-5 - 8
10X-RAY DIFFRACTION5E9 - 144
11X-RAY DIFFRACTION6F-5 - 24
12X-RAY DIFFRACTION6F25 - 144

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