[English] 日本語
Yorodumi
- PDB-5f7u: Cycloalternan-forming enzyme from Listeria monocytogenes in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f7u
TitleCycloalternan-forming enzyme from Listeria monocytogenes in complex with pentasaccharide substrate
ComponentsCycloalternan-forming enzyme
KeywordsSUGAR BINDING PROTEIN / Complex / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Carbohydrate binding module (family 35) / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 ...Carbohydrate binding module (family 35) / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Lmo2446 protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLight, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Nat Microbiol / Year: 2016
Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis.
Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cycloalternan-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,91311
Polymers118,5941
Non-polymers2,31910
Water24,5001360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint10 kcal/mol
Surface area36420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.222, 100.894, 71.812
Angle α, β, γ (deg.)90.00, 104.01, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Cycloalternan-forming enzyme / Lmo2446 protein


Mass: 118593.812 Da / Num. of mol.: 1 / Mutation: D565N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2446 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8Y4J2

-
Sugars , 4 types, 5 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-3[DGlcpa1-6]DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a3-b1_a6-d1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 1365 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1360 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: Crystallization condition: JCSG+ suite (Qiagen) A5: 200 mM Magnesium formate and 20% w/v PEG3350 Protein solution: 7.0 mg/mL in 10 mM Tris/HCl pH 8.3, 500 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 127612 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMQ

4kmq


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.735 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18997 6444 5 %RANDOM
Rwork0.15932 ---
obs0.16085 121168 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.326 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20.01 Å2
2---0.48 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8335 0 153 1360 9848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028792
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.94711991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80751078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55925.573445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.445151321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3791525
X-RAY DIFFRACTIONr_chiral_restr0.0910.21310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216828
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_it0.4661.2994285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7941.9475372
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.821.4364507
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.15113.2115218
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: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 450 -
Rwork0.257 8786 -
obs--98.21 %
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)
11.6226-0.75780.20661.7545-0.11041.4562-0.0001-0.18890.06180.1450.0434-0.1672-0.081-0.0413-0.04340.0604-0.0267-0.0180.03670.00120.0204-38.042810.508448.9006
20.6512-0.27340.2491.3401-0.13531.2871-0.0418-0.02390.04120.05020.010.1418-0.1449-0.1090.03190.0480.02030.01510.0138-0.00370.0479-65.768730.456622.5537
32.62781.47731.45913.00681.72152.409-0.0716-0.18460.2260.1489-0.08290.2313-0.0763-0.20370.15450.07650.00820.02510.0389-0.00340.0479-60.701120.757932.1177
40.4917-0.1977-0.02640.51590.10540.44570.01010.03330.02520.0255-0.0137-0.0809-0.02750.10060.00360.0116-0.0128-0.00570.04030.01550.0227-39.27024.087511.2005
50.64720.11660.14150.4413-0.01350.67690.00580.16820.0195-0.0917-0.00120.0588-0.03260.0347-0.00460.02530.0123-0.01580.0658-0.00120.0172-60.69820.3027-10.0966
66.0938-1.49361.09628.2478-1.86073.18180.08360.2589-0.3335-0.3193-0.0043-0.01830.286-0.0385-0.07930.161-0.00680.00830.1558-0.03420.0241-58.1922-5.2335-33.5622
71.80121.132-0.80692.0579-0.93121.4131-0.00940.2115-0.0628-0.13550.0048-0.0090.04250.13340.00460.08240.0343-0.05030.1473-0.02160.0366-67.343-4.5234-22.3458
81.9531-0.8478-0.4571.86640.721.92820.0820.1543-0.2175-0.0829-0.07430.13690.3525-0.0509-0.00760.12280.0172-0.0690.0657-0.03890.0939-83.7517-16.3192-17.6536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 144
2X-RAY DIFFRACTION2A145 - 247
3X-RAY DIFFRACTION3A248 - 275
4X-RAY DIFFRACTION4A276 - 721
5X-RAY DIFFRACTION5A722 - 919
6X-RAY DIFFRACTION6A920 - 934
7X-RAY DIFFRACTION7A935 - 979
8X-RAY DIFFRACTION8A980 - 1091

+
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