[English] 日本語
Yorodumi
- PDB-6blg: Crystal Structure of Sugar Transaminase from Klebsiella pneumonia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6blg
TitleCrystal Structure of Sugar Transaminase from Klebsiella pneumoniae Complexed with PLP
ComponentsdTDP-4-amino-4,6-dideoxygalactose transaminase
KeywordsTRANSFERASE / pyridoxal phosphate (PLP)-dependent sugar aminotransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


dTDP-4-amino-4,6-dideoxygalactose transaminase / dTDP-4-amino-4,6-dideoxygalactose transaminase activity / enterobacterial common antigen biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
dTDP-4-amino-4,6-dideoxygalactose transaminase WecE-like / dTDP-4-amino-4,6-dideoxygalactose transaminase WecE / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...dTDP-4-amino-4,6-dideoxygalactose transaminase WecE-like / dTDP-4-amino-4,6-dideoxygalactose transaminase WecE / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / dTDP-4-amino-4,6-dideoxygalactose transaminase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsMaltseva, N. / Kim, Y. / Shatsman, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: To Be Published
Title: Crystal Structure of Sugar Transaminase from Klebsiella pneumoniae Complexed with PLP
Authors: Maltseva, N. / Kim, Y. / Shatsman, S. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dTDP-4-amino-4,6-dideoxygalactose transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,78814
Polymers42,7561
Non-polymers1,03213
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: dTDP-4-amino-4,6-dideoxygalactose transaminase
hetero molecules

A: dTDP-4-amino-4,6-dideoxygalactose transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,57528
Polymers85,5112
Non-polymers2,06426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8320 Å2
ΔGint-232 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.853, 130.853, 138.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-405-

SO4

21A-406-

SO4

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein dTDP-4-amino-4,6-dideoxygalactose transaminase


Mass: 42755.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: wecE, KPN_04291 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold
References: UniProt: A6TGH9, dTDP-4-amino-4,6-dideoxygalactose transaminase

-
Non-polymers , 6 types, 65 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.67 Å3/Da / Density % sol: 53.99 % / Description: cube
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M Ammonium sulfate, 0.1M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2017 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→37.77 Å / Num. obs: 26700 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 48.07 Å2 / CC1/2: 0.748 / Rsym value: 0.07 / Net I/σ(I): 18.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1324 / Rsym value: 0.894 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZAH

4zah


Resolution: 2.102→37.767 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 24.02
RfactorNum. reflection% reflection
Rfree0.2253 1364 5.11 %
Rwork0.1748 --
obs0.1774 26689 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.4 Å2
Refinement stepCycle: LAST / Resolution: 2.102→37.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 55 52 3088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063129
X-RAY DIFFRACTIONf_angle_d0.7494245
X-RAY DIFFRACTIONf_dihedral_angle_d19.921855
X-RAY DIFFRACTIONf_chiral_restr0.048461
X-RAY DIFFRACTIONf_plane_restr0.005544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1017-2.17680.32771270.26222489X-RAY DIFFRACTION99
2.1768-2.2640.27871300.22542525X-RAY DIFFRACTION100
2.264-2.3670.29141380.21462496X-RAY DIFFRACTION100
2.367-2.49180.22271260.19552521X-RAY DIFFRACTION100
2.4918-2.64790.22721370.2012519X-RAY DIFFRACTION100
2.6479-2.85220.28131450.20942522X-RAY DIFFRACTION100
2.8522-3.13920.27181500.21362523X-RAY DIFFRACTION100
3.1392-3.59310.26321330.19712536X-RAY DIFFRACTION100
3.5931-4.52570.20671500.14172549X-RAY DIFFRACTION100
4.5257-37.77310.16581280.14622645X-RAY DIFFRACTION100
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)
18.1268-2.1503-4.50961.37430.23833.2492-0.43920.0973-0.42-0.03250.22090.04470.80790.1510.29660.6487-0.0083-0.03630.4008-0.06380.46826.649721.2168-2.4112
25.90210.83770.7553.5668-4.40435.9415-0.29850.5315-0.2092-0.60940.0508-0.03450.7346-0.07080.2160.48430.02010.0470.4844-0.0810.28639.963430.702-15.1098
31.7401-0.28490.21071.28970.78721.9592-0.03920.14750.4669-0.09130.0813-0.0008-0.2786-0.0114-0.03620.4265-0.0140.02890.32660.04690.418610.823753.331-5.967
42.3735-1.6368-0.94740.70620.24181.18540.03750.2376-0.0143-0.028-0.00970.00270.02130.1855-0.00050.4442-0.0248-0.03230.4311-0.02270.347812.718437.9611-11.0479
56.02711.70783.60321.64140.79824.90260.30440.51560.3592-0.5138-0.10750.116-0.22350.7195-0.1360.66590.0741-0.01280.483-0.00890.426429.035233.4932-13.3124
66.4706-4.7882-2.20034.59471.44921.52910.17820.2614-0.3712-0.2027-0.18460.26780.0918-0.13080.03680.4629-0.03660.01420.3542-0.01950.4233-6.939833.4388-4.2198
73.66251.2758-0.54032.583-0.66615.07870.17330.1690.3706-0.0775-0.09960.231-0.4999-0.2498-0.06770.40320.02390.02680.3958-0.01770.5034-10.165847.81270.8083
83.65453.6171-2.3324.0538-1.4765.5897-0.0834-0.52380.38750.1808-0.13950.3-0.0721-0.16030.29090.37410.03910.05070.3709-0.02560.3467-4.719645.128614.501
95.28952.46150.46594.1790.05280.850.0473-0.35770.5408-0.08640.00410.4909-0.1992-0.0701-0.05470.42690.02640.05730.3451-0.01650.3298-5.144846.72747.3939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 236 )
6X-RAY DIFFRACTION6chain 'A' and (resid 237 through 273 )
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 299 )
8X-RAY DIFFRACTION8chain 'A' and (resid 300 through 327 )
9X-RAY DIFFRACTION9chain 'A' and (resid 328 through 376 )

+
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