[English] 日本語
Yorodumi
- PDB-7xhp: Structure of a Glucose 6-Phosphate Dehydrogenase from Zymomonas m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xhp
TitleStructure of a Glucose 6-Phosphate Dehydrogenase from Zymomonas mobilis
ComponentsGlucose 6-Phosphate Dehydrogenase
KeywordsOXIDOREDUCTASE / Nicotinamide cofactor
Function / homologyDihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsMeng, D.D. / Liu, M.X. / Liu, W.D. / You, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778073 China
CitationJournal: Acs Catalysis / Year: 2023
Title: Coenzyme Engineering of Glucose-6-phosphate Dehydrogenase on a Nicotinamide-Based Biomimic and Its Application as a Glucose Biosensor
Authors: Meng, D.D. / Liu, M.X. / Su, H. / Song, H.Y. / Chen, L.J. / Li, Q.Z. / Liu, Y.N. / Zhu, Z.G. / Liu, W.D. / Sheng, X. / You, C. / Zhang, Y.H.
History
DepositionApr 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucose 6-Phosphate Dehydrogenase
B: Glucose 6-Phosphate Dehydrogenase
C: Glucose 6-Phosphate Dehydrogenase
D: Glucose 6-Phosphate Dehydrogenase
E: Glucose 6-Phosphate Dehydrogenase
F: Glucose 6-Phosphate Dehydrogenase
G: Glucose 6-Phosphate Dehydrogenase
H: Glucose 6-Phosphate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)440,5328
Polymers440,5328
Non-polymers00
Water2,018112
1
A: Glucose 6-Phosphate Dehydrogenase
B: Glucose 6-Phosphate Dehydrogenase
C: Glucose 6-Phosphate Dehydrogenase
D: Glucose 6-Phosphate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)220,2664
Polymers220,2664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-108 kcal/mol
Surface area69430 Å2
MethodPISA
2
E: Glucose 6-Phosphate Dehydrogenase
F: Glucose 6-Phosphate Dehydrogenase
G: Glucose 6-Phosphate Dehydrogenase
H: Glucose 6-Phosphate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)220,2664
Polymers220,2664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-112 kcal/mol
Surface area79990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.610, 101.073, 321.066
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 30 or resid 37...
21(chain B and (resid 7 through 10 or (resid 11...
31(chain E and (resid 7 through 10 or (resid 11...
41(chain F and (resid 7 through 10 or (resid 11...
51(chain G and (resid 7 through 10 or (resid 11...
61(chain H and (resid 7 through 10 or (resid 11...
12(chain C and (resid 139 through 143 or (resid 144...
22(chain D and (resid 139 through 271 or (resid 272...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 through 30 or resid 37...A7 - 30
121(chain A and (resid 7 through 30 or resid 37...A37 - 78
131(chain A and (resid 7 through 30 or resid 37...A80 - 98
141(chain A and (resid 7 through 30 or resid 37...A99
151(chain A and (resid 7 through 30 or resid 37...A6 - 487
161(chain A and (resid 7 through 30 or resid 37...A6 - 487
171(chain A and (resid 7 through 30 or resid 37...A6 - 487
181(chain A and (resid 7 through 30 or resid 37...A6 - 487
191(chain A and (resid 7 through 30 or resid 37...A6 - 487
1101(chain A and (resid 7 through 30 or resid 37...A6 - 487
211(chain B and (resid 7 through 10 or (resid 11...B7 - 10
221(chain B and (resid 7 through 10 or (resid 11...B11
231(chain B and (resid 7 through 10 or (resid 11...B6 - 487
241(chain B and (resid 7 through 10 or (resid 11...B6 - 487
251(chain B and (resid 7 through 10 or (resid 11...B6 - 487
261(chain B and (resid 7 through 10 or (resid 11...B1
271(chain B and (resid 7 through 10 or (resid 11...B6 - 487
281(chain B and (resid 7 through 10 or (resid 11...B6 - 487
291(chain B and (resid 7 through 10 or (resid 11...B6 - 487
2101(chain B and (resid 7 through 10 or (resid 11...B6 - 487
2111(chain B and (resid 7 through 10 or (resid 11...B6 - 487
2121(chain B and (resid 7 through 10 or (resid 11...B6 - 487
311(chain E and (resid 7 through 10 or (resid 11...E7 - 10
321(chain E and (resid 7 through 10 or (resid 11...E11
331(chain E and (resid 7 through 10 or (resid 11...E4 - 487
341(chain E and (resid 7 through 10 or (resid 11...E4 - 487
351(chain E and (resid 7 through 10 or (resid 11...E4 - 487
361(chain E and (resid 7 through 10 or (resid 11...E4 - 487
411(chain F and (resid 7 through 10 or (resid 11...F7 - 10
421(chain F and (resid 7 through 10 or (resid 11...F11
431(chain F and (resid 7 through 10 or (resid 11...F8 - 487
441(chain F and (resid 7 through 10 or (resid 11...F8 - 487
451(chain F and (resid 7 through 10 or (resid 11...F8 - 487
461(chain F and (resid 7 through 10 or (resid 11...F8 - 487
511(chain G and (resid 7 through 10 or (resid 11...G7 - 10
521(chain G and (resid 7 through 10 or (resid 11...G11
531(chain G and (resid 7 through 10 or (resid 11...G3 - 487
541(chain G and (resid 7 through 10 or (resid 11...G3 - 487
551(chain G and (resid 7 through 10 or (resid 11...G3 - 487
561(chain G and (resid 7 through 10 or (resid 11...G1
571(chain G and (resid 7 through 10 or (resid 11...G3 - 487
581(chain G and (resid 7 through 10 or (resid 11...G3 - 487
591(chain G and (resid 7 through 10 or (resid 11...G3 - 487
5101(chain G and (resid 7 through 10 or (resid 11...G3 - 487
5111(chain G and (resid 7 through 10 or (resid 11...G3 - 487
5121(chain G and (resid 7 through 10 or (resid 11...G3 - 487
611(chain H and (resid 7 through 10 or (resid 11...H7 - 10
621(chain H and (resid 7 through 10 or (resid 11...H11
631(chain H and (resid 7 through 10 or (resid 11...H2 - 487
641(chain H and (resid 7 through 10 or (resid 11...H2 - 487
651(chain H and (resid 7 through 10 or (resid 11...H2 - 487
661(chain H and (resid 7 through 10 or (resid 11...H3
671(chain H and (resid 7 through 10 or (resid 11...H46
681(chain H and (resid 7 through 10 or (resid 11...H2 - 487
691(chain H and (resid 7 through 10 or (resid 11...H2 - 487
6101(chain H and (resid 7 through 10 or (resid 11...H2 - 487
6111(chain H and (resid 7 through 10 or (resid 11...H2 - 487
6121(chain H and (resid 7 through 10 or (resid 11...H2 - 487
112(chain C and (resid 139 through 143 or (resid 144...C139 - 143
122(chain C and (resid 139 through 143 or (resid 144...C144
132(chain C and (resid 139 through 143 or (resid 144...C139 - 487
142(chain C and (resid 139 through 143 or (resid 144...C139 - 487
152(chain C and (resid 139 through 143 or (resid 144...C139 - 487
162(chain C and (resid 139 through 143 or (resid 144...C139 - 487
212(chain D and (resid 139 through 271 or (resid 272...D139 - 271
222(chain D and (resid 139 through 271 or (resid 272...D272 - 273
232(chain D and (resid 139 through 271 or (resid 272...D123 - 493
242(chain D and (resid 139 through 271 or (resid 272...D123 - 493
252(chain D and (resid 139 through 271 or (resid 272...D123 - 493
262(chain D and (resid 139 through 271 or (resid 272...D374
272(chain D and (resid 139 through 271 or (resid 272...D374
282(chain D and (resid 139 through 271 or (resid 272...D123 - 493
292(chain D and (resid 139 through 271 or (resid 272...D123 - 493
2102(chain D and (resid 139 through 271 or (resid 272...D123 - 493
2112(chain D and (resid 139 through 271 or (resid 272...D123 - 493

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Glucose 6-Phosphate Dehydrogenase


Mass: 55066.500 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate (pH 6.0), 10% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.78→78.18 Å / Num. obs: 218096 / % possible obs: 85.4 % / Redundancy: 2.433 % / CC1/2: 0.986 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.117 / Χ2: 0.893 / Net I/σ(I): 7.43 / Num. measured all: 530641 / Scaling rejects: 7
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
2.78-2.851.8680.4081.562751718908147330.480.53277.9
2.85-2.932.1660.3282.213464718410159980.6340.41786.9
2.93-3.012.3210.2812.763635217971156610.7440.35387.1
3.01-3.112.3520.243.33561717338151420.7890.30187.3
3.11-3.212.4020.1954.13539916868147390.8650.24387.4
3.21-3.322.440.1615.183477916314142530.9090.20187.4
3.32-3.452.4650.1436.193367015663136620.920.17787.2
3.45-3.592.4930.1227.563307015231132660.9430.15187.1
3.59-3.752.4780.1158.333076814445124150.950.14385.9
3.75-3.932.3740.1029.092784913863117330.9560.12884.6
3.93-4.142.3670.09310.172635113168111330.9660.11784.5
4.14-4.392.5460.08611.492751412522108060.9710.10686.3
4.39-4.72.7340.08212.732745011720100400.9720.10185.7
4.7-5.072.7580.08212.84255641092592700.9720.184.9
5.07-5.562.7520.08112.6223323998584740.9740.09984.9
5.56-6.212.6950.07912.6120887916677510.9740.09684.6
6.21-7.182.5760.07312.6617237797566910.9780.0983.9
7.18-8.792.430.06612.8813518673155620.9780.08282.6
8.79-12.432.8860.06414.412922520644770.9850.07786
12.43-78.182.710.05413.496207287322900.9890.06779.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 600000000 / Resolution: 2.78→78.18 Å / Cross valid method: THROUGHOUT / σ(F): 85.51 / Phase error: 30.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2893 6412 5.43 %
Rwork0.2334 112227 -
obs0.2394 118103 90.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.75 Å2 / Biso mean: 55.4972 Å2 / Biso min: 28.41 Å2
Refinement stepCycle: final / Resolution: 2.78→78.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26238 0 0 112 26350
Biso mean---49.79 -
Num. residues----3483
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7755X-RAY DIFFRACTION16.514TORSIONAL
12B7755X-RAY DIFFRACTION16.514TORSIONAL
13E7755X-RAY DIFFRACTION16.514TORSIONAL
14F7755X-RAY DIFFRACTION16.514TORSIONAL
15G7755X-RAY DIFFRACTION16.514TORSIONAL
16H7755X-RAY DIFFRACTION16.514TORSIONAL
21C2052X-RAY DIFFRACTION16.514TORSIONAL
22D2052X-RAY DIFFRACTION16.514TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.78-2.830.34872630.30225155541880
2.83-2.880.33643110.2995816612788
2.88-2.930.30813090.28825646595588
2.93-2.990.33062950.28395702599788
2.99-3.060.33953010.28945724602589
3.06-3.130.33933040.28425677598188
3.13-3.210.31332950.27695729602488
3.21-3.30.32432910.27795707599888
3.3-3.390.31922940.26395704599888
3.39-3.50.3053000.25895726602687
3.5-3.630.32852900.26135580587087
3.63-3.770.29092920.24675579587186
3.77-3.940.28082900.23615483577384
3.94-4.150.30942900.22595556584686
4.15-4.410.26722940.21265671596587
4.41-4.750.24653010.19695679598087
4.75-5.230.26172850.21045560584586
5.23-5.990.26882950.22435567586285
5.99-7.540.30082810.2285500578183
7.55-78.180.27772950.20425466576181

+
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