[English] 日本語
Yorodumi
- PDB-6bzc: Crystal Structure of Glucose-6-phosphate Isomerase from Elizabeth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bzc
TitleCrystal Structure of Glucose-6-phosphate Isomerase from Elizabethkingia anophelis with bound Glucose-6-phosphate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / gluconeogenesis / carbohydrate biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative binding / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Glucose-6-phosphate Isomerase from Elizabethkingia anophelis with bound Glucose-6-phosphate
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8289
Polymers125,9672
Non-polymers8617
Water9,782543
1
A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5226
Polymers62,9841
Non-polymers5385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3063
Polymers62,9841
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-62 kcal/mol
Surface area35130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.280, 102.140, 153.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glucose-6-phosphate isomerase / / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 62983.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: pgi, BD94_3890 / Plasmid: ElanA.17127.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A077EQ93, glucose-6-phosphate isomerase
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: ElanA.17127.a.B1.PS38341 at 26.1 mg/ml was mixed 1:1 with MCSG1(f1): 0.1 M Bis-Tris:HCl, pH=6.5, 20% (w/v) PEG MME 5000. Crystal was then soaked with 5 mM glucose-6-phosphate and 20% ...Details: ElanA.17127.a.B1.PS38341 at 26.1 mg/ml was mixed 1:1 with MCSG1(f1): 0.1 M Bis-Tris:HCl, pH=6.5, 20% (w/v) PEG MME 5000. Crystal was then soaked with 5 mM glucose-6-phosphate and 20% ethylene glycol for 4 days. Tray: 295124f1, puck: pqf5-1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→48.466 Å / Num. obs: 68995 / % possible obs: 99.7 % / Redundancy: 4.004 % / Biso Wilson estimate: 24.64 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.119 / Χ2: 0.98 / Net I/σ(I): 9.51 / Num. measured all: 276270 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.14.0580.5082.5720399502950270.7260.587100
2.1-2.164.0690.4173.320116495249440.7820.48199.8
2.16-2.224.0720.3593.7919496479647880.8430.41599.8
2.22-2.294.0850.3234.2818945464746380.8710.37299.8
2.29-2.374.0750.2844.9118425452645220.8980.32899.9
2.37-2.454.0740.2475.7317691434843420.9030.28699.9
2.45-2.544.0710.2176.317145422042120.9390.25199.8
2.54-2.654.060.1897.2516600409840890.9460.21999.8
2.65-2.764.0380.1618.3315854393039260.9610.18699.9
2.76-2.93.9910.1369.5714919374237380.9740.15799.9
2.9-3.063.9860.11411.3314137355435470.9790.13299.8
3.06-3.243.9230.09513.1813304340333910.9830.1199.6
3.24-3.473.9090.0815.6912436319431810.9880.09299.6
3.47-3.743.8690.0717.5911440297229570.9890.08199.5
3.74-4.13.8660.06518.8810659277227570.990.07599.5
4.1-4.583.9140.05920.259667249524700.990.06899
4.58-5.293.9340.05520.168666222322030.9940.06399.1
5.29-6.483.9110.05118.97442190619030.9940.05999.8
6.48-9.173.9010.04120.115816149514910.9970.04799.7
9.17-48.4663.5820.0320.4631138908690.9980.03497.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(dev_2919)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZB

6bzb


Resolution: 2.05→48.466 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 2075 3.01 %
Rwork0.2069 66919 -
obs0.209 68994 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.27 Å2 / Biso mean: 29.6201 Å2 / Biso min: 9.53 Å2
Refinement stepCycle: final / Resolution: 2.05→48.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8699 0 54 548 9301
Biso mean--35.83 29.51 -
Num. residues----1094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0499-2.09760.33151450.262144134558100
2.0976-2.15010.32621370.255743704507100
2.1501-2.20820.33471530.254844094562100
2.2082-2.27320.35511280.251744104538100
2.2732-2.34650.32451450.250644194564100
2.3465-2.43040.3161200.240344494569100
2.4304-2.52770.33941470.235844154562100
2.5277-2.64280.35831410.232544194560100
2.6428-2.78210.32571470.22444554602100
2.7821-2.95640.30341550.216144344589100
2.9564-3.18460.30791180.215144974615100
3.1846-3.5050.26061110.19464491460299
3.505-4.01190.23481460.180944834629100
4.0119-5.05380.22091470.16724510465799
5.0538-48.47920.20121350.178347454880100
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)
12.7743-1.40920.08813.63550.59731.1261-0.07460.17130.0273-0.48370.147-0.1283-0.1459-0.1334-0.06460.3013-0.03760.05450.31550.04650.150126.972812.5942-44.3986
21.06630.13170.31690.38240.45541.3157-0.11930.13550.1605-0.1192-0.0652-0.0534-0.30740.15980.15170.3214-0.08320.03130.23220.07990.27230.610726.7537-27.0274
30.8143-0.0043-0.3330.47130.1451.32360.0054-0.0891-0.0607-0.00060.0176-0.08070.0720.2067-0.01280.1816-0.0291-0.0130.23880.04610.239732.83487.8501-2.2083
42.72-0.2131.27070.9788-0.41963.0468-0.0285-0.3392-0.14950.16070.10440.12040.0061-0.1777-0.08640.2284-0.01190.04180.22840.05680.211125.154710.42657.6782
50.6815-0.13410.2260.90370.05020.8171-0.00580.07990.1414-0.0296-0.05-0.0473-0.06390.07040.05510.1693-0.04190.02590.1960.04330.180530.32414.0181-19.8884
60.57830.3626-0.09841.0420.26910.41690.01560.0878-0.0814-0.2176-0.0214-0.0004-0.02350.009-0.00360.225-0.01240.02830.2379-0.03170.157224.87350.6955-31.1317
70.76710.33920.06380.55450.15370.5566-0.02020.045-0.0682-0.05390.02130.0238-0.0003-0.02630.00350.17120.0175-0.02050.21840.03430.169815.59953.283-25.2562
80.2015-0.192-0.02921.21540.1650.948-0.04370.0484-0.0595-0.1697-0.00260.2892-0.1482-0.21660.05340.1927-0.0184-0.03090.4070.00390.332-8.96330.5388-26.4454
91.5385-0.60950.07272.968-0.40332.0929-0.03810.0519-0.2567-0.17220.01330.25080.2543-0.15260.00040.278-0.0747-0.02770.2391-0.02750.27912.4937-25.752-26.3626
101.19910.2791-0.31240.7886-0.23550.7935-0.11860.1238-0.1604-0.0357-0.0136-0.14590.28660.06910.1330.31-0.00490.01690.20630.04670.245623.3873-22.6494-13.1092
110.31080.0840.18940.5770.16910.65720.02890.01450.004-0.02090.03110.10350.0445-0.1013-0.04570.1814-0.0010.01030.2510.01230.22536.90170.1834-20.2423
124.1365-1.4203-2.3365.46451.07376.25960.3141-0.09230.6822-0.15990.06180.051-0.4485-0.102-0.32270.2066-0.00210.02450.20530.0190.23555.096331.8516-17.481
130.7043-0.1979-0.19310.6207-0.1620.5089-0.0092-0.015-0.1311-0.1289-0.01140.01260.04320.07890.02480.2099-0.05280.01660.25040.00150.23619.2634-7.9507-29.3232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 59 )A0 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 116 )A60 - 116
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 212 )A117 - 212
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 243 )A213 - 243
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 356 )A244 - 356
6X-RAY DIFFRACTION6chain 'A' and (resid 357 through 432 )A357 - 432
7X-RAY DIFFRACTION7chain 'A' and (resid 433 through 547 )A433 - 547
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 72 )B2 - 72
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 116 )B73 - 116
10X-RAY DIFFRACTION10chain 'B' and (resid 117 through 305 )B117 - 305
11X-RAY DIFFRACTION11chain 'B' and (resid 306 through 432 )B306 - 432
12X-RAY DIFFRACTION12chain 'B' and (resid 433 through 460 )B433 - 460
13X-RAY DIFFRACTION13chain 'B' and (resid 461 through 547 )B461 - 547

+
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