[English] 日本語
Yorodumi
- PDB-5lu6: Heptose isomerase mutant - H64Q -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lu6
TitleHeptose isomerase mutant - H64Q
ComponentsPhosphoheptose isomeraseD-sedoheptulose 7-phosphate isomerase
KeywordsISOMERASE / Cooperativity / enzyme kinetics / hydrogen bonds / molecular modelling / quantum mechanics
Function / homology
Function and homology information


D-sedoheptulose-7-phosphate isomerase / D-sedoheptulose 7-phosphate isomerase activity / D-glycero-D-manno-heptose 7-phosphate biosynthetic process / capsule polysaccharide biosynthetic process / carbohydrate derivative binding / carbohydrate metabolic process / zinc ion binding / cytoplasm
Similarity search - Function
Phosphoheptose isomerase / GmhA/DiaA / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE / TRIETHYLENE GLYCOL / Phosphoheptose isomerase / Phosphoheptose isomerase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 Å
AuthorsVivoli, M. / Harmer, N.J. / Pang, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society2009/R2 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: A half-site multimeric enzyme achieves its cooperativity without conformational changes.
Authors: Vivoli, M. / Pang, J. / Harmer, N.J.
History
DepositionSep 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoheptose isomerase
B: Phosphoheptose isomerase
C: Phosphoheptose isomerase
D: Phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,68417
Polymers82,7864
Non-polymers1,89713
Water12,592699
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18090 Å2
ΔGint-51 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.610, 84.610, 127.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPHEPHEAA3 - 1943 - 194
21ASNASNPHEPHEBB3 - 1943 - 194
12ARGARGPHEPHEAA4 - 1944 - 194
22ARGARGPHEPHECC4 - 1944 - 194
13ASNASNPHEPHEAA3 - 1943 - 194
23ASNASNPHEPHEDD3 - 1943 - 194
14ARGARGPHEPHEBB4 - 1944 - 194
24ARGARGPHEPHECC4 - 1944 - 194
15ASNASNLYSLYSBB3 - 1963 - 196
25ASNASNLYSLYSDD3 - 1963 - 196
16ARGARGPHEPHECC4 - 1944 - 194
26ARGARGPHEPHEDD4 - 1944 - 194

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Phosphoheptose isomerase / D-sedoheptulose 7-phosphate isomerase / Sedoheptulose 7-phosphate isomerase


Mass: 20696.604 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: gmhA, DP49_467 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A095TT41, UniProt: Q93UJ2*PLUS, D-sedoheptulose-7-phosphate isomerase

-
Non-polymers , 5 types, 712 molecules

#2: Chemical
ChemComp-I22 / D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE / 7-O-PHOSPHONO-D-ALTRO-HEPT-2-ULOSE / SEDOHEPTULOSE 7-PHOSPHATE / Sedoheptulose 7-phosphate


Mass: 290.162 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H15O10P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: batch mode
Details: untagge GmhA 10 mg per ml 0.1 M Na Acetate, pH 4.6, 8% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.67→63.7 Å / Num. obs: 1322870 / % possible obs: 88.6 % / Redundancy: 6.4 % / Net I/σ(I): 7.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 1.67→42.31 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.458 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22599 3881 5 %RANDOM
Rwork0.1892 ---
obs0.19104 73739 83.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.814 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--0.52 Å2-0 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 1.67→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 120 699 6509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195942
X-RAY DIFFRACTIONr_bond_other_d0.010.025792
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9888024
X-RAY DIFFRACTIONr_angle_other_deg1.636313311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4324.298242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39115989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3411541
X-RAY DIFFRACTIONr_chiral_restr0.1080.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026792
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021289
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_it1.7551.7853118
X-RAY DIFFRACTIONr_mcbond_other1.7471.7833116
X-RAY DIFFRACTIONr_mcangle_it2.3942.6633892
X-RAY DIFFRACTIONr_mcangle_other2.3942.6643893
X-RAY DIFFRACTIONr_scbond_it2.8362.2092824
X-RAY DIFFRACTIONr_scbond_other2.8352.2092824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2333.1594125
X-RAY DIFFRACTIONr_long_range_B_refined5.72318.05626432
X-RAY DIFFRACTIONr_long_range_B_other5.72318.05726433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A109040.09
12B109040.09
21A109750.09
22C109750.09
31A107390.11
32D107390.11
41B108200.1
42C108200.1
51B107230.12
52D107230.12
61C108210.11
62D108210.11
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 300 -
Rwork0.247 5666 -
obs--88.4 %

+
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