[English] 日本語
Yorodumi
- PDB-4xj7: Crystal Structure of E112A Mutant of Stationary Phase Survival Pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xj7
TitleCrystal Structure of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium soaked with AMP
Components5'/3'-nucleotidase SurE
KeywordsHYDROLASE / Stationary phase survival protein / Domain swapping / Rossmann fold like / Phosphatase
Function / homology
Function and homology information


3'-nucleotidase / exopolyphosphatase / 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase 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
ADENINE / ADENOSINE / PHOSPHATE ION / 5'/3'-nucleotidase SurE
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMathiharan, Y.K. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein.
Authors: Mathiharan, Y.K. / Savithri, H.S. / Murthy, M.R.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
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_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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'/3'-nucleotidase SurE
B: 5'/3'-nucleotidase SurE
C: 5'/3'-nucleotidase SurE
D: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,65118
Polymers114,2284
Non-polymers1,42314
Water24,9511385
1
A: 5'/3'-nucleotidase SurE
B: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,93910
Polymers57,1142
Non-polymers8258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-93 kcal/mol
Surface area21470 Å2
MethodPISA
2
C: 5'/3'-nucleotidase SurE
D: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7128
Polymers57,1142
Non-polymers5986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-99 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.620, 95.780, 94.750
Angle α, β, γ (deg.)90.00, 100.07, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
5'/3'-nucleotidase SurE / Exopolyphosphatase / Nucleoside monophosphate phosphohydrolase


Mass: 28557.074 Da / Num. of mol.: 4 / Mutation: E112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: surE, STM2927 / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS
References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase, exopolyphosphatase

-
Non-polymers , 6 types, 1399 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1385 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.2M sodium citrate tribasic dihydrate, 0.1M Tris (pH 8.5), 30% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2013 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.6→24.89 Å / Num. obs: 184243 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 21.479 Å2 / Rsym value: 0.054 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RYU

4ryu


Resolution: 1.6→24.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.671 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20798 9164 5 %RANDOM
Rwork0.17498 175028 --
obs0.17663 175028 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20.15 Å2
2--0.04 Å20 Å2
3----0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.6→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7656 0 90 1385 9131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9711267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1851099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1423.908348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.302151194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7551560
X-RAY DIFFRACTIONr_chiral_restr0.1110.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216412
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 663 -
Rwork0.304 12583 -
obs--98.07 %

+
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://pdbjlvh1.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