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- PDB-3ty2: Structure of a 5'-nucleotidase (surE) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3ty2
TitleStructure of a 5'-nucleotidase (surE) from Coxiella burnetii
Components5'-nucleotidase surE
KeywordsHYDROLASE / survival protein / phosphatase
Function / homology
Function and homology information


UMP catabolic process / 3'-nucleotidase activity / exopolyphosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Stationary-phase Survival Protein Sure Homolog; Chain: A, / Survival protein SurE-like phosphatase/nucleotidase / Survival protein SurE / Survival protein SurE-like phosphatase/nucleotidase / SurE-like phosphatase/nucleotidase superfamily / Survival protein SurE / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-nucleotidase SurE
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.885 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-nucleotidase surE
B: 5'-nucleotidase surE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5153
Polymers57,3932
Non-polymers1221
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-49 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.331, 95.953, 69.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

21A-386-

HOH

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Components

#1: Protein 5'-nucleotidase surE / Nucleoside 5'-monophosphate phosphohydrolase


Mass: 28696.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: surE, CBU_1671 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KI21, 5'-nucleotidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris, 0.05M Lithium sulfate, 50% PEG 200, pH 7.0, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 20, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.885→50 Å / Num. all: 41859 / Num. obs: 40897 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.041 / Χ2: 1.016 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.885-1.932.60.26316090.482178.4
1.93-1.972.90.25217750.497185.8
1.97-2.013.20.19918950.551192.5
2.01-2.053.90.18520240.533197.1
2.05-2.094.80.16720480.615199.9
2.09-2.145.10.14120510.6281100
2.14-2.195.20.12220660.6821100
2.19-2.255.20.1120900.6921100
2.25-2.325.20.09920660.7641100
2.32-2.395.30.08820490.7951100
2.39-2.485.30.07921100.8241100
2.48-2.585.30.0720800.8681100
2.58-2.75.40.06220860.9541100
2.7-2.845.40.05920751.0141100
2.84-3.025.40.0521101.1561100
3.02-3.255.50.04320831.211100
3.25-3.585.50.03721221.3821100
3.58-4.097.20.03821321.5211100
4.09-5.1610.80.03521531.4661100
5.16-509.90.02922731.265199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2V4N

2v4n


Resolution: 1.885→39.402 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8166 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 2052 5.05 %random
Rwork0.1991 ---
all0.2014 44279 --
obs0.2014 40602 96.33 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.316 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 235.74 Å2 / Biso mean: 33.936 Å2 / Biso min: 8.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.5671 Å20 Å20 Å2
2---1.5698 Å20 Å2
3---2.1369 Å2
Refinement stepCycle: LAST / Resolution: 1.885→39.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 8 235 4089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054051
X-RAY DIFFRACTIONf_angle_d0.9315541
X-RAY DIFFRACTIONf_chiral_restr0.064627
X-RAY DIFFRACTIONf_plane_restr0.004733
X-RAY DIFFRACTIONf_dihedral_angle_d11.811506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.885-1.92890.3561820.28741832191470
1.9289-1.97720.28811280.25992287241588
1.9772-2.03060.32951350.22832538267396
2.0306-2.09040.27591480.221526282776100
2.0904-2.15780.28321340.201726362770100
2.1578-2.2350.27021370.208626292766100
2.235-2.32440.28951450.203826262771100
2.3244-2.43020.25531540.215526202774100
2.4302-2.55830.26491470.2022611275899
2.5583-2.71860.2431360.20292609274598
2.7186-2.92840.2441340.21542633276798
2.9284-3.2230.24691280.20922655278398
3.223-3.68910.23541460.193427052851100
3.6891-4.64670.20661380.16172705284399
4.6467-39.41020.22671600.19822836299699
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)
10.22560.0193-0.07730.2942-0.08960.15340.0604-0.18-0.0043-0.0715-0.03270.01550.10150.0967-0.02340.1656-0.0374-0.01090.2136-0.00360.117832.107338.825434.0584
20.17680.0746-0.11240.1647-0.0440.1234-0.07460.0285-0.0402-0.09150.07390.10470.1095-0.0118-0.01740.1203-0.018-0.01150.09910.03760.115325.342733.315628.1528
30.17780.06860.01340.03780.00940.35560.1654-0.00960.22170.0085-0.04050.02080.0389-0.011-0.05020.1883-0.02350.05110.1405-0.00310.273418.111840.97334.5134
40.8261-0.0922-0.21430.3498-0.44390.7020.07-0.2205-0.20650.1482-0.01960.0566-0.01250.1483-0.02140.1953-0.04840.02220.25530.02240.214616.206632.975743.1211
50.2140.1318-0.06340.0928-0.10030.158-0.04860.00280.0940.0657-0.05110.10560.0933-0.09320.01450.1937-0.00340.08260.16030.0080.262210.575734.896336.9007
60.3256-0.19110.03140.19030.14350.39040.0469-0.04210.1115-0.07120.08580.0759-0.0828-0.17250.07690.2771-0.0461-0.06870.22870.10610.229819.736354.816415.034
70.15650.3064-0.14240.6719-0.35250.2569-0.06380.04820.3199-0.06640.40080.4432-0.0801-0.1525-0.10950.1745-0.0406-0.01820.28930.10240.32288.504238.284624.3902
80.9344-0.12390.08451.06330.63180.40990.02650.1886-0.1948-0.1867-0.20020.1066-0.0346-0.15640.07760.3203-0.0992-0.03530.3511-0.02320.29559.906523.6671-1.4179
90.45270.1281-0.16230.4378-0.24070.3851-0.17170.14430.0924-0.04040.049-0.0817-0.1806-0.04190.03930.2229-0.0404-0.04050.20040.04260.173525.919647.54013.1211
100.0535-0.0433-00.2813-0.15681.2476-0.01270.0936-0.2639-0.0890.1417-0.162-0.0534-0.24490.08410.1688-0.0298-0.03610.2155-0.09650.254621.771433.39590.6734
110.14440.14930.00910.15740.03730.02650.0205-0.0035-0.1784-0.03780.0079-0.06110.06080.0452-0.05550.2353-0.0565-0.15230.0799-0.08350.259726.960921.43665.5716
120.07440.0161-0.10380.16670.09540.2592-0.1713-0.03760.12540.0776-0.1754-0.2002-0.28150.13140.14590.2351-0.0304-0.09710.16490.02390.330949.044735.498226.1113
130.26470.05880.241-0.00610.0520.19540.3993-0.0129-0.56180.13840.0438-0.31530.35520.03690.23660.2031-0.145-0.2163-0.019-0.27950.290723.413522.25648.6111
140.59940.0693-0.06381.01510.0080.3645-0.16570.10790.04580.12130.0590.3026-0.0088-0.040.02350.1959-0.03890.00940.23650.02470.26235.821325.609334.4962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 11:77)A11 - 77
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 78:125)A78 - 125
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 126:142)A126 - 142
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 143:159)A143 - 159
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 160:185)A160 - 185
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 186:210)A186 - 210
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 211:245)A211 - 245
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 246:261)A246 - 261
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 11:95)B11 - 95
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 96:176)B96 - 176
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 177:197)B177 - 197
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 198:210)B198 - 210
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 211:245)B211 - 245
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 246:261)B246 - 261

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