[English] 日本語
Yorodumi
- PDB-8zn4: Crystal structure of Poly(ethylene glycol) stabilized erythrose-4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zn4
TitleCrystal structure of Poly(ethylene glycol) stabilized erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 2.30 A resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsViswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Sharma, S. / Raje, C.I. / Singh, T.P.
Funding support India, 2items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
Indian Council of Medical Research India
CitationJournal: To Be Published
Title: Crystal structure of Poly(ethylene glycol) stabilized erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 2.30 A resolution
Authors: Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Sharma, S. / Raje, C.I. / Singh, T.P.
History
DepositionMay 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,70553
Polymers152,2504
Non-polymers7,45549
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31150 Å2
ΔGint-52 kcal/mol
Surface area46030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.775, 167.135, 150.103
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 38062.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_ ...Gene: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_18430, EA706_09520, EA720_004470, EGM95_14355, F4T85_07645, FDN00_13975, FE003_13215, FJU42_18405, FJV09_11310, GSE42_06795, HBK86_03865, IAG11_16195, SAMEA4394745_03679
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A059ZTK9, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

-
Non-polymers , 11 types, 690 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H42O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: A reservoir solution containing 0.2 M MgCl2.6H2O, 0.1 M HEPES sodium (pH 7.5), and 30% v/v PEG 400 was prepared.

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.3→46.703 Å / Num. obs: 81357 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.02 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4423 / CC1/2: 0.82 / Rpim(I) all: 0.47 / Rrim(I) all: 1.69 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMC

3cmc


Resolution: 2.3→46.703 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.142 / SU B: 6.136 / SU ML: 0.145 / Average fsc free: 0.9678 / Average fsc work: 0.9803 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.201 2400 2.951 %
Rwork0.1517 78921 -
all0.153 --
obs-81321 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.028 Å2
Baniso -1Baniso -2Baniso -3
1-1.561 Å20 Å2-0 Å2
2---3.614 Å20 Å2
3---2.053 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 488 641 11845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211448
X-RAY DIFFRACTIONr_bond_other_d0.0050.01610983
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.79715481
X-RAY DIFFRACTIONr_angle_other_deg0.521.75425214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00851370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.827576
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.24154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.205101866
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.57110508
X-RAY DIFFRACTIONr_chiral_restr0.0710.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022554
X-RAY DIFFRACTIONr_nbd_refined0.2010.22079
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.210184
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25361
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.26096
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2563
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2590.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.221
X-RAY DIFFRACTIONr_nbd_other0.2030.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.26
X-RAY DIFFRACTIONr_mcbond_it3.5914.2395479
X-RAY DIFFRACTIONr_mcbond_other3.594.2395479
X-RAY DIFFRACTIONr_mcangle_it5.1447.6016848
X-RAY DIFFRACTIONr_mcangle_other5.1437.6036849
X-RAY DIFFRACTIONr_scbond_it4.9884.9585969
X-RAY DIFFRACTIONr_scbond_other4.9884.9595970
X-RAY DIFFRACTIONr_scangle_it7.5288.788633
X-RAY DIFFRACTIONr_scangle_other7.5288.7818634
X-RAY DIFFRACTIONr_lrange_it9.59341.00812168
X-RAY DIFFRACTIONr_lrange_other9.58441.00712085
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.2521810.2357950.23159770.9450.95899.98330.209
2.36-2.4240.2671660.21656280.21757950.9520.96599.98270.197
2.424-2.4940.2271700.18854280.18955980.9650.9741000.168
2.494-2.5710.2541570.18853340.1954930.9570.97499.96360.168
2.571-2.6550.2681570.18251640.18453230.9630.97899.96240.16
2.655-2.7480.2191550.16750100.16951650.9650.9811000.147
2.748-2.8510.2151410.15548170.15749590.9730.98499.97980.137
2.851-2.9670.2071250.1646620.16147870.9750.9841000.142
2.967-3.0980.251380.15844500.1645880.9610.9841000.142
3.098-3.2490.2321380.16542740.16844120.9660.9831000.15
3.249-3.4240.1881220.14540640.14641860.9790.9871000.134
3.424-3.630.2191220.15438680.15639910.9680.98599.97490.146
3.63-3.8790.2321080.15136350.15337440.9680.98699.97330.144
3.879-4.1870.1791000.12533960.12734960.9790.991000.122
4.187-4.5830.146990.10831290.10932280.9890.9931000.11
4.583-5.1180.155950.11928320.1229270.9860.9921000.121
5.118-5.8980.169820.14425270.14526090.9860.9891000.144
5.898-7.1950.2580.14821770.14922350.9820.9881000.148
7.195-10.0570.136550.12317040.12317590.990.9911000.131
10.057-46.7030.218310.20110270.20110650.9580.97399.34270.211

+
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