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- PDB-5hzz: Crystal structure of DR2231_E47A mutant in complex with dUMP and ... -

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Basic information

Entry
Database: PDB / ID: 5hzz
TitleCrystal structure of DR2231_E47A mutant in complex with dUMP and manganese
ComponentsDR2231
KeywordsHYDROLASE / alpha helix
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
: / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / HAD superfamily Cof-like phosphohydrolase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.801 Å
AuthorsMota, C.S. / Goncalves, A.M.D. / de Sanctis, D.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e TecnologiaSFRH/BEST/51724/2011 Portugal
CitationJournal: FEBS J. / Year: 2016
Title: Deinococcus radiodurans DR2231 is a two-metal-ion mechanism hydrolase with exclusive activity on dUTP.
Authors: Mota, C.S. / Goncalves, A.M. / de Sanctis, D.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,72712
Polymers64,7814
Non-polymers9468
Water16,376909
1
A: DR2231
C: DR2231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8636
Polymers32,3902
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-70 kcal/mol
Surface area13780 Å2
MethodPISA
2
B: DR2231
D: DR2231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8636
Polymers32,3902
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-73 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.452, 77.893, 52.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
DR2231


Mass: 16195.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Gene: DR_2231 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9RS96
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / 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: 2.5 Å3/Da / Density % sol: 50.74 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: Lithium Acetate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.801→43.59 Å / Num. all: 57527 / Num. obs: 57527 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.73 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Rsym value: 0.046 / Net I/av σ(I): 12.481 / Net I/σ(I): 18.8 / Num. measured all: 213560
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.93.70.2712.83060481880.160.3160.2714.998
1.9-2.013.80.1654.73005079180.0970.1930.1657.899.8
2.01-2.153.80.1047.42801773940.0610.1210.10411.899.7
2.15-2.333.80.07110.72605469230.0420.0830.07116.299.6
2.33-2.553.70.05513.52408264220.0330.0640.05520.199.5
2.55-2.853.70.04416.22161858170.0260.0510.04424.399.5
2.85-3.293.70.03618.41880051420.0210.0420.0363099.1
3.29-4.033.60.0320.41546743360.0180.0350.0335.898.5
4.03-5.73.50.02719.81215734360.0170.0320.02737.298.9
5.7-43.593.40.0227.7671119510.0130.0240.0236.796.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.16data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 2YFC

2yfc


Resolution: 1.801→43.59 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 2917 5.08 %
Rwork0.1633 54540 -
obs0.1655 57457 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.51 Å2 / Biso mean: 24.3282 Å2 / Biso min: 4.26 Å2
Refinement stepCycle: final / Resolution: 1.801→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 46 909 5225
Biso mean--11.86 34.33 -
Num. residues----559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064460
X-RAY DIFFRACTIONf_angle_d0.7926046
X-RAY DIFFRACTIONf_chiral_restr0.044675
X-RAY DIFFRACTIONf_plane_restr0.006816
X-RAY DIFFRACTIONf_dihedral_angle_d17.6011658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8013-1.83090.32961260.2742428255494
1.8309-1.86240.27591380.226725892727100
1.8624-1.89630.28891300.20262579270999
1.8963-1.93280.21521510.187425852736100
1.9328-1.97220.23291460.1822548269499
1.9722-2.01510.26111350.171426052740100
2.0151-2.0620.2081410.17112567270899
2.062-2.11350.19421540.159525832737100
2.1135-2.17070.17541380.15412566270499
2.1707-2.23460.1981310.15352597272899
2.2346-2.30670.24591310.158826012732100
2.3067-2.38910.2081390.15632602274199
2.3891-2.48480.23311380.168225932731100
2.4848-2.59780.23171430.16772600274399
2.5978-2.73480.21391350.16912610274599
2.7348-2.90610.23281370.16262625276299
2.9061-3.13040.20911290.15862622275199
3.1304-3.44530.20041250.15192624274999
3.4453-3.94360.16611390.1442621276098
3.9436-4.96740.15921560.13962650280698
4.9674-43.60270.20811550.17512745290097
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)
10.02790.01840.02990.00760.00590.01180.0502-0.0767-0.10930.1103-0.1199-0.0935-0.01850.0688-00.1296-0.025-0.02610.16640.0120.1013-12.5071-26.2136-14.3002
20.3178-0.0875-0.08950.0338-0.02940.1405-0.0453-0.16450.33970.0221-0.03860.1007-0.11440.0439-0.01880.1459-0.0568-0.02530.0697-0.04210.1758-25.798-11.201-23.5274
30.2145-0.10920.13840.06240.09390.1910.0515-0.0708-0.01390.0035-0.0528-0.00430.0806-0.0073-0.02010.1146-0.0302-0.03470.08180.00890.0825-28.5689-25.9571-27.2963
40.0156-0.00620.01120.01590.02250.05570.0124-0.0581-0.05220.0807-0.0319-0.0228-0.044-0.0432-0.01750.2017-0.0831-0.04680.18340.05520.1252-24.9137-37.7376-9.68
50.0110.00020.00150.0015-0.00810.0007-0.01130.04590.0083-0.02350.03360.089-0.0079-0.1300.0977-0.0444-0.01460.1731-0.00240.1487-69.5439-28.9724-6.4219
60.0052-0.00170.00110.0025-0.005-0.0014-0.0120.09020.0097-0.0734-0.05330.06090.0703-0.030700.1849-0.0042-0.02330.332900.2006-64.2132-27.7721-18.8055
70.52180.118-0.18430.1315-0.0270.2174-0.23580.43160.4955-0.09030.2546-0.1027-0.0616-0.25680.01230.08280.1261-0.0612-0.0999-0.00130.2405-55.1057-12.2278-2.4468
80.00320.003800.0060.0014-0.00040.004-0.01920.01990.03290.0151-0.0242-0.0016-0.024700.4069-0.0266-0.07380.3983-0.16760.2896-55.3818-10.067719.943
90.13440.02110.02940.0262-0.05210.1062-0.0172-0.05760.02750.01650.0302-0.00790.1005-0.1889-0.0080.0891-0.0083-0.02890.1032-0.00330.1184-57.1311-26.3241-2.1687
100.00470.00190.0080.00070.00170.00060.0141-0.0823-0.046-0.04280.0275-0.0234-0.02-0.08630.00090.0935-0.0082-0.01230.05540.01510.0958-38.453-27.64847.7991
110.00740.00190.00070.0064-0.0010.00180.09110.0252-0.050.01370.044-0.03090.06420.07450.00040.1229-0.0158-0.02760.0897-0.01630.1246-36.6957-32.92013.1067
120.002-0.00030.00130.00290.00270.00260.00130.02340.0014-0.02370.0346-0.03780.0580.022900.17420.013-0.03340.1281-0.03290.134-40.7915-37.4648-5.8737
130.0323-0.0028-0.00020.01360.02180.0306-0.02060.108-0.0346-0.0019-0.0346-0.04320.0103-0.1314-0.01270.0643-0.0681-0.13640.1074-0.1827-0.0469-53.806-38.9061-16.4924
14-0.0027-0.0039-0.0010.00080.0031-0.0044-0.03730.1483-0.07140.0450.0638-0.0867-0.01490.043100.15540.0188-0.01070.1323-0.03280.2644-11.3742-47.365-35.7263
150.03910.02970.02510.01320.00640.00620.0530.1316-0.0065-0.0523-0.0332-0.00720.15050.1320.00040.12930.0183-0.03250.1015-0.01170.1011-25.9225-28.5975-38.0332
160.18830.076-0.00560.06290.02290.01490.0505-0.1550.18480.0477-0.01480.08170.0513-0.02130.03780.1058-0.0285-0.00110.1304-0.06590.116-32.9061-19.324-17.4055
170.2716-0.05650.15310.1564-0.11160.19580.10090.04650.0425-0.1379-0.1764-0.10450.10250.1763-0.05960.0074-0.0598-0.03090.0877-0.0010.0472-15.617-20.2669-28.0766
18-0.003-0.00070.00260.0027-0.009-0.0071-0.1061-0.0061-0.005-0.01040.07770.00940.12150.090100.1832-0.0040.00820.17560.01630.1979-62.1143-47.19338.6958
190.0254-0.03080.02440.02210.01410.01370.0393-0.1903-0.01920.0872-0.04280.03030.1645-0.17-0.00760.1123-0.0389-0.00720.13470.01080.0919-53.7151-29.887311.6274
200.5262-0.0933-0.13610.09330.0590.1740.1370.31040.362-0.0375-0.012-0.09430.0128-0.04970.11550.0591-0.0398-0.03020.04670.05260.1284-47.074-19.997-8.9629
210.1874-0.00660.17210.0941-0.00120.072-0.0243-0.0460.03960.0304-0.03040.04520.0159-0.1754-0.01760.07140.0029-0.00630.1546-0.02270.1022-64.5444-22.10041.8637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 33 )A7 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 63 )A34 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 133 )A64 - 133
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 144 )A134 - 144
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 20 )B6 - 20
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 33 )B21 - 33
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 63 )B34 - 63
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 70 )B64 - 70
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 112 )B71 - 112
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 122 )B113 - 122
11X-RAY DIFFRACTION11chain 'B' and (resid 123 through 127 )B123 - 127
12X-RAY DIFFRACTION12chain 'B' and (resid 128 through 133 )B128 - 133
13X-RAY DIFFRACTION13chain 'B' and (resid 134 through 144 )B134 - 144
14X-RAY DIFFRACTION14chain 'C' and (resid -4 through 9 )C-4 - 9
15X-RAY DIFFRACTION15chain 'C' and (resid 10 through 33 )C10 - 33
16X-RAY DIFFRACTION16chain 'C' and (resid 34 through 69 )C34 - 69
17X-RAY DIFFRACTION17chain 'C' and (resid 70 through 144 )C70 - 144
18X-RAY DIFFRACTION18chain 'D' and (resid -4 through 9 )D-4 - 9
19X-RAY DIFFRACTION19chain 'D' and (resid 10 through 33 )D10 - 33
20X-RAY DIFFRACTION20chain 'D' and (resid 34 through 69 )D34 - 69
21X-RAY DIFFRACTION21chain 'D' and (resid 70 through 144 )D70 - 144

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