[English] 日本語
Yorodumi
- PDB-5z2k: Structure of S38A mutant Mn-bound periplasmic metal binding prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z2k
TitleStructure of S38A mutant Mn-bound periplasmic metal binding protein from candidatus liberibacter asiaticus
ComponentsPeriplasmic solute binding protein
KeywordsMETAL BINDING PROTEIN / ABC Transporter / Periplasmic solute binding protein
Function / homology
Function and homology information


metal ion transport / cell envelope / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Periplasmic solute binding protein
Similarity search - Component
Biological speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaini, G. / Sharma, N. / Dalal, V. / Kumar, P. / Sharma, A.K.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: The analysis of subtle internal communications through mutation studies in periplasmic metal uptake protein CLas-ZnuA2
Authors: Saini, G. / Sharma, N. / Dalal, V. / Warghane, A. / Ghosh, D.K. / Kumar, P. / Sharma, A.K.
History
DepositionJan 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,03116
Polymers30,8811
Non-polymers1,15015
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-12 kcal/mol
Surface area13020 Å2
2
A: Periplasmic solute binding protein
hetero molecules

A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,06232
Polymers61,7622
Non-polymers2,30030
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5860 Å2
ΔGint-34 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.190, 94.190, 94.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Periplasmic solute binding protein


Mass: 30881.055 Da / Num. of mol.: 1 / Mutation: S38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Liberibacter asiaticus (strain psy62) (bacteria)
Strain: psy62 / Gene: CLIBASIA_02120 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C6XF58

-
Non-polymers , 5 types, 391 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M SODIUM ACETATE TRIHYDRATE PH 4.6, 2M AMMONIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 30, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→81.58 Å / Num. obs: 44692 / % possible obs: 97.9 % / Redundancy: 5.7 % / Net I/σ(I): 20.6
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.1 / % possible all: 85.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UDO

4udo


Resolution: 1.8→81.58 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.1 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1645 2254 5 %RANDOM
Rwork0.14548 ---
obs0.14647 42404 99.48 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 26.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.8→81.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 72 376 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192387
X-RAY DIFFRACTIONr_bond_other_d0.0020.022232
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9863247
X-RAY DIFFRACTIONr_angle_other_deg0.99135216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4135305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82924.84899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51915422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7031511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212650
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02453
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_it2.3541.3851164
X-RAY DIFFRACTIONr_mcbond_other2.1071.3531156
X-RAY DIFFRACTIONr_mcangle_it3.3282.0161467
X-RAY DIFFRACTIONr_mcangle_other3.3312.021468
X-RAY DIFFRACTIONr_scbond_it3.5731.7851221
X-RAY DIFFRACTIONr_scbond_other3.5711.7881222
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.222.5171774
X-RAY DIFFRACTIONr_long_range_B_refined8.68920.0562915
X-RAY DIFFRACTIONr_long_range_B_other8.70120.0712916
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 154 -
Rwork0.215 2926 -
obs--93.53 %
Refinement TLS params.Method: refined / Origin x: 29.371 Å / Origin y: -27.284 Å / Origin z: 20.787 Å
111213212223313233
T0.0329 Å2-0.0032 Å2-0.0058 Å2-0.0185 Å20.0031 Å2--0.0193 Å2
L0.9901 °2-0.2365 °2-0.2655 °2-1.5574 °20.2546 °2--1.1421 °2
S-0.0145 Å °0.0578 Å °0.07 Å °-0.0329 Å °-0.0171 Å °0.0467 Å °-0.1484 Å °-0.0171 Å °0.0316 Å °

+
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