[English] 日本語
Yorodumi
- PDB-3p3v: Crystal structure of a PTS dependent N-acetyl-galactosamine-IIB c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p3v
TitleCrystal structure of a PTS dependent N-acetyl-galactosamine-IIB component (agaV, SPy_0631) from Streptococcus pyogenes at 1.65 A resolution
ComponentsPTS system, N-acetylgalactosamine-specific IIB component
KeywordsTRANSFERASE / PTS IIB COMPONENT / PHOSPHOTRANSFERASE / SUGAR TRANSPORT / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Putative PTS dependent N-acetyl-galactosamine-IIB component
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a PTS dependent N-acetyl-galactosamine-IIB component (agaV, SPy_0631) from Streptococcus pyogenes at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: PTS system, N-acetylgalactosamine-specific IIB component
B: PTS system, N-acetylgalactosamine-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6536
Polymers36,1852
Non-polymers4694
Water5,278293
1
A: PTS system, N-acetylgalactosamine-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1982
Polymers18,0921
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PTS system, N-acetylgalactosamine-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4554
Polymers18,0921
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.139, 80.696, 47.213
Angle α, β, γ (deg.)90.000, 105.260, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC STATE IN SOLUTION.

-
Components

#1: Protein PTS system, N-acetylgalactosamine-specific IIB component / Putative PTS dependent N-acetyl-galactosamine-IIB component


Mass: 18092.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: agaV, M5005_Spy0521, SPy_0631 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: Q9A0T4, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30.00% polyethylene glycol 6000, 0.1M HEPES pH 7.0, Additive: 0.005 M Mannose, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.96109,0.97934,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961091
20.979341
30.97921
ReflectionResolution: 1.65→28.638 Å / Num. all: 36409 / Num. obs: 36409 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.718 Å2 / Rsym value: 0.059 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.693.60.4911.6972426780.49199
1.69-1.743.60.3842945425950.38498.8
1.74-1.793.60.2962.6912425140.29698.7
1.79-1.843.70.2413.2901824640.24199.1
1.84-1.913.60.1764.4874824020.17699.2
1.91-1.973.70.145.4845123130.1499.1
1.97-2.053.70.1096.7817222350.10999.5
2.05-2.133.70.0947.6792821670.09499.3
2.13-2.223.70.0877.5762620820.08799.5
2.22-2.333.70.0827.7727719820.08299.6
2.33-2.463.70.0827.5688018780.08299.5
2.46-2.613.70.0738.3656517870.07399.7
2.61-2.793.70.0610.5616316780.0699.8
2.79-3.013.70.05311.9576615750.05399.9
3.01-3.33.70.04414.5521314210.04499.9
3.3-3.693.70.0415.4488013280.0499.9
3.69-4.263.70.0415.1427811690.0499.9
4.26-5.223.70.03616.635759770.03699.9
5.22-7.383.60.04116.327557610.04199.9
7.38-28.6383.40.0416.613584030.0492.3

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→28.638 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.65 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. POLYETHYLENE GLYCOL (PEG AND PGE) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 1816 5 %RANDOM
Rwork0.1584 ---
obs0.1602 36401 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.36 Å2 / Biso mean: 26.7488 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å21.16 Å2
2---0.93 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 31 293 2812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222636
X-RAY DIFFRACTIONr_bond_other_d0.0010.021716
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9533592
X-RAY DIFFRACTIONr_angle_other_deg0.90234269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9445348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23525.701107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.715466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.895159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_mcbond_it1.7731668
X-RAY DIFFRACTIONr_mcbond_other0.5343669
X-RAY DIFFRACTIONr_mcangle_it2.93152748
X-RAY DIFFRACTIONr_scbond_it4.5228968
X-RAY DIFFRACTIONr_scangle_it6.75911834
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 119 -
Rwork0.228 2546 -
all-2665 -
obs--98.96 %
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)
10.673-0.1715-0.24991.20040.14581.75710.0085-0.01040.0480.0577-0.0042-0.01360.0535-0.0094-0.00430.04010.0088-0.00430.016-0.00550.005134.60984.544424.7974
21.1823-0.4410.29471.6644-0.36660.7012-0.0324-0.01170.02590.05610.05020.1833-0.0137-0.0511-0.01780.00760.0001-0.00370.0609-0.00530.042523.763621.59937.2609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 162
2X-RAY DIFFRACTION2B0 - 162

+
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