[English] 日本語
Yorodumi
- PDB-3ty2: Structure of a 5'-nucleotidase (surE) from Coxiella burnetii -

+
Open data


ID or keywords:

Loading...

-
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


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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more