[English] 日本語
Yorodumi
- PDB-3ty1: Crystal structure of a putative aldose 1-epimerase (KPN_04629) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ty1
TitleCrystal structure of a putative aldose 1-epimerase (KPN_04629) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.90 A resolution
ComponentsHypothetical aldose 1-epimerase
KeywordsISOMERASE / Supersandwich / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4432 / Domain of unknown function (DUF4432) / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / carbohydrate binding / Mainly Beta / Thioredoxin-like protein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical aldose 1-epimerase (KPN_04629) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Feb 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
Revision 1.4Oct 16, 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: Hypothetical aldose 1-epimerase
B: Hypothetical aldose 1-epimerase
C: Hypothetical aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,79729
Polymers128,5033
Non-polymers2,29426
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-260 kcal/mol
Surface area39550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.033, 119.953, 103.015
Angle α, β, γ (deg.)90.000, 106.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-722-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING SUPPORT THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Hypothetical aldose 1-epimerase / Putative thioredoxin-like protein


Mass: 42834.219 Da / Num. of mol.: 3 / Fragment: UNP residues 20-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: trxC, KPN78578_45560, KPN_04629 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6THE6

-
Non-polymers , 5 types, 804 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 20-402) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 20-402) 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40.00% 2-methyl-2,4-pentanediol, 0.20M ammonium sulfate, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97932,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 23, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
30.979151
ReflectionResolution: 1.9→29.698 Å / Num. all: 113332 / Num. obs: 113332 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.331 Å2 / Rsym value: 0.074 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.953.80.5612.33164683630.561100
1.95-23.80.4352.83116881980.435100
2-2.063.80.3523.43010979090.352100
2.06-2.123.80.342907676480.3100
2.12-2.193.80.2354.82857074790.235100
2.19-2.273.80.1965.82769572720.196100
2.27-2.363.80.1666.32650369200.166100
2.36-2.453.80.1417.22575467260.141100
2.45-2.563.80.12582463064140.125100
2.56-2.693.80.1119.62375761920.111100
2.69-2.833.80.10410.92245058380.104100
2.83-33.80.091132136955580.091100
3-3.213.80.07415.72003352110.074100
3.21-3.473.80.06318.31867248540.063100
3.47-3.83.80.05220.61716444620.052100
3.8-4.253.80.04422.41566140690.044100
4.25-4.913.80.04424.11371735700.044100
4.91-6.013.80.04823.51163630320.048100
6.01-8.53.80.04622.6904323670.046100
8.5-29.6983.70.03824.9456812500.03895.2

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.698 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.177 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.114
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.2-METHYL-2,4-PENTANEDIOL (MPD) AND SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION AND CHLORIDE (CL) FROM THE PURIFICATION BUFFER HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 5671 5 %RANDOM
Rwork0.1581 ---
obs0.1598 113323 99.96 %-
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: 137.89 Å2 / Biso mean: 47.1879 Å2 / Biso min: 19.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.23 Å2
2---1.32 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8927 0 132 778 9837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229413
X-RAY DIFFRACTIONr_bond_other_d0.0020.026174
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.95612853
X-RAY DIFFRACTIONr_angle_other_deg1.232315164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68751199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83625.217437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.059151531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7881537
X-RAY DIFFRACTIONr_chiral_restr0.1010.21418
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021799
X-RAY DIFFRACTIONr_mcbond_it1.77235803
X-RAY DIFFRACTIONr_mcbond_other0.54432373
X-RAY DIFFRACTIONr_mcangle_it2.859379
X-RAY DIFFRACTIONr_scbond_it4.85583610
X-RAY DIFFRACTIONr_scangle_it6.86113451
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 446 -
Rwork0.25 7885 -
all-8331 -
obs--99.99 %
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)
10.82110.52230.22561.34650.47220.7895-0.00330.04310.1412-0.0665-0.0760.37410.0072-0.13960.07920.01390.0024-0.04070.0976-0.00970.147925.1852-7.7025-1.7702
21.00320.75590.23751.6950.40060.66950.1187-0.07940.00620.2313-0.032-0.19-0.0490.0493-0.08670.054-0.0202-0.01810.0425-0.02320.048556.830711.88618.3998
31.05510.70690.00561.47330.4091.02430.423-0.45130.29590.8436-0.47810.48690.2708-0.27230.05510.5013-0.30890.28410.3554-0.17760.169424.3471-3.590440.2154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 402
2X-RAY DIFFRACTION2B0 - 402
3X-RAY DIFFRACTION3C0 - 402

+
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