[English] 日本語
Yorodumi
- PDB-3d5p: CRYSTAL STRUCTURE OF A PUTATIVE GLUCAN SYNTHESIS REGULATOR OF SMI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d5p
TitleCRYSTAL STRUCTURE OF A PUTATIVE GLUCAN SYNTHESIS REGULATOR OF SMI1/KNR4 FAMILY (BF1740) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.45 A RESOLUTION
Componentsputative glucan synthesis regulator of Smi1/Knr4 family
KeywordsGENE REGULATION / PUTATIVE GLUCAN SYNTHESIS REGULATOR OF SMI1/KNR4 FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


SMI1/KNR4-like / SMI1/KNR4-like / SMI1 / KNR4 family (SUKH-1) / Knr4/Smi1-like domain / SMI1 / KNR4 family / Knr4/Smi1-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative glucan synthesis regulator of Smi1/Knr4 family (YP_211376.1) from Bacteroides fragilis NCTC 9343 at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: putative glucan synthesis regulator of Smi1/Knr4 family
B: putative glucan synthesis regulator of Smi1/Knr4 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6629
Polymers33,1022
Non-polymers5607
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-17 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.058, 69.508, 75.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIC STATE.

-
Components

#1: Protein putative glucan synthesis regulator of Smi1/Knr4 family


Mass: 16551.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: YP_211376.1, BF1740 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LEL2
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97916,0.97852
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979161
30.978521
ReflectionResolution: 1.45→29.683 Å / Num. obs: 52450 / % possible obs: 98 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.17 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.493.30.5581.41064632060.55883
1.49-1.533.60.4831.61350437050.48397.5
1.53-1.573.70.3961.91361536670.39698.6
1.57-1.623.70.3262.31323635530.32698.7
1.62-1.673.70.2592.91284434650.25999.1
1.67-1.733.70.2183.51249933540.21898.8
1.73-1.83.70.1764.21199332310.17699.2
1.8-1.873.70.14951160031220.14999.4
1.87-1.963.70.1136.51127730310.11399.4
1.96-2.053.70.0947.51070028850.09499.4
2.05-2.163.70.07691016527380.07699.7
2.16-2.293.70.06610.1975026300.06699.6
2.29-2.453.70.0611.5904624450.0699.8
2.45-2.653.70.05511.8856823220.05599.8
2.65-2.93.70.0512.8784321360.0599.9
2.9-3.243.70.04314.3713419390.04399.9
3.24-3.743.70.03915.2630217210.03999.5
3.74-4.593.60.03516.7525914650.03599.7
4.59-6.483.50.03815.8413711760.03899.8
6.48-29.683.40.0412.922156590.0496.7

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→29.683 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.001 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.061
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ACETATE (ACT) IONS, GLYCEROL (GOL) AND PEG4000 FRAGMENT (PEG) MOLECULES FROM CRYSTALLIZATION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 2676 5.1 %RANDOM
Rwork0.156 ---
obs0.157 52409 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.475 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 37 335 2510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222474
X-RAY DIFFRACTIONr_bond_other_d0.0010.021618
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9563374
X-RAY DIFFRACTIONr_angle_other_deg1.41833974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07125.478115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59115412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.154153
X-RAY DIFFRACTIONr_chiral_restr0.1070.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022880
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02519
X-RAY DIFFRACTIONr_mcbond_it1.36921488
X-RAY DIFFRACTIONr_mcbond_other0.3752612
X-RAY DIFFRACTIONr_mcangle_it2.2532403
X-RAY DIFFRACTIONr_scbond_it1.8472986
X-RAY DIFFRACTIONr_scangle_it2.7183971
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 181 -
Rwork0.238 3020 -
all-3201 -
obs--82.01 %
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)
10.4467-0.1259-0.03661.23990.29170.4093-0.01450.01660.003-0.1295-0.06320.1283-0.0932-0.09440.0777-0.01150.0177-0.0268-0.0176-0.0183-0.025347.006442.366112.3956
20.39040.05780.08260.54320.09510.35840.001-0.0028-0.0480.038-0.01260.03770.0088-0.04070.0116-0.0218-0.0041-0.0033-0.0073-0.0064-0.014550.07316.93789.1665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1321 - 133
2X-RAY DIFFRACTION2BB0 - 1321 - 133

+
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