[English] 日本語
Yorodumi
- PDB-3om4: Crystal structure of B. megaterium levansucrase mutant K373A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3om4
TitleCrystal structure of B. megaterium levansucrase mutant K373A
ComponentsLevansucrase
KeywordsTRANSFERASE / five fold beta-propeller / levansucrase
Function / homology
Function and homology information


levansucrase / levansucrase activity / carbohydrate utilization / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 68 / Levansucrase/Invertase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Levansucrase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsStrube, C.P. / Homann, A. / Gamer, M. / Jahn, D. / Seibel, J. / Heinz, D.W.
CitationJournal: To be Published
Title: Crystal structure of B. megaterium levansucrase mutant K373A
Authors: Strube, C.P. / Homann, A. / Gamer, M. / Jahn, D. / Seibel, J. / Heinz, D.W.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Levansucrase
B: Levansucrase
C: Levansucrase
D: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,84721
Polymers204,0594
Non-polymers1,78817
Water26,2481457
1
A: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4075
Polymers51,0151
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4515
Polymers51,0151
Non-polymers4364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5916
Polymers51,0151
Non-polymers5775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3975
Polymers51,0151
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.585, 100.075, 95.544
Angle α, β, γ (deg.)90.000, 90.670, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Levansucrase


Mass: 51014.801 Da / Num. of mol.: 4 / Fragment: Levansucrase SacB, UNP residues 29-484 / Mutation: K373A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: sacB / Production host: Escherichia coli (E. coli) / References: UniProt: D5DC07, levansucrase

-
Non-polymers , 6 types, 1474 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1457 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: USING 3 uL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3 uL RESERVOIR BUFFER (0.1 M Na-Phosphate-citrate pH 4.1; 0.2 M lithiumsulfate; 20% (w/v) PEG 1000) IN THE DROPLET. , VAPOR DIFFUSION, ...Details: USING 3 uL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3 uL RESERVOIR BUFFER (0.1 M Na-Phosphate-citrate pH 4.1; 0.2 M lithiumsulfate; 20% (w/v) PEG 1000) IN THE DROPLET. , VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MX-225 ccd-detector from Rayonics (Evanston, USA) / Detector: CCD / Date: Apr 24, 2009
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.75→47.77 Å / Num. all: 174958 / Num. obs: 172859 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.75→1.84 Å / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→47.77 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.279 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 8763 5 %RANDOM
Rwork0.2015 ---
all0.202 174958 --
obs0.202 174956 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.51 Å2 / Biso mean: 13.2493 Å2 / Biso min: 3.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.38 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14152 0 104 1457 15713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214672
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.94519864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06151822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36525.855743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.563152473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5191536
X-RAY DIFFRACTIONr_chiral_restr0.0710.22109
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111320
X-RAY DIFFRACTIONr_mcbond_it0.391.58934
X-RAY DIFFRACTIONr_mcangle_it0.727214431
X-RAY DIFFRACTIONr_scbond_it0.86535738
X-RAY DIFFRACTIONr_scangle_it1.4674.55425
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 643 -
Rwork0.292 12145 -
all-12788 -
obs--97.92 %

+
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