[English] 日本語
Yorodumi
- PDB-9ijb: Crystal structure and function analysis of a highly potential dru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ijb
TitleCrystal structure and function analysis of a highly potential drug target 6-phosphogluconate dehydrogenase in Mycobacterium tuberculosis
Components6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating
KeywordsHYDROLASE / Tecramer / Dehydrogenase Enzyme / NAD binding / pentose phosphate pathway
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) / organic acid catabolic process / D-gluconate metabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt / NADP binding
Similarity search - Function
6-phosphogluconate dehydrogenase, YqeC-type / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7404051296 Å
AuthorsWang, Y.Z. / Ren, X.Q. / Li, T. / Zhang, R.D.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2017YFA0504300 China
National Natural Science Foundation of China (NSFC)2017YFA0505900 China
National Natural Science Foundation of China (NSFC)32360046 China
CitationJournal: To Be Published
Title: Crystal structure and function analysis of a potential drug target 6-phosphogluconate dehydrogenase in Mycobacterium tuberculosis
Authors: Wang, Y.Z. / Ren, X.Q. / Li, T. / Zhang, R.D.
History
DepositionJun 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating
B: 6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating
C: 6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating
D: 6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating


Theoretical massNumber of molelcules
Total (without water)145,6004
Polymers145,6004
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29610 Å2
ΔGint-209 kcal/mol
Surface area45070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.991, 107.246, 137.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating / 6-phosphogluconate dehydrogenase / decarboxylating


Mass: 36400.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 6-phosphogluconate dehydrogenase / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: gnd2, gntZ, A4S10_01196, ERS007681_00218, ERS007718_03264, ERS007720_01707, ERS007741_00547, ERS027646_01529, ERS027661_00118, ERS035788_00611, ERS053720_03175, SAMEA2683035_02610
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A045IPA0, phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating), phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 22.5% PEG3350, 100 mM di-Sodium malonate, 100 mM Tris (pH 8.0)

-
Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 37669 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 60.2835318425 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.049 / Rrim(I) all: 0.171 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.75-2.812.50.97218390.8480.9580.2830.0150.427100
2.8-2.8512.60.88718440.9360.9830.2580.9250.4499.9
2.85-2.912.60.8118560.8840.9690.2360.8440.44699.9
2.9-2.9612.60.73418560.9150.9770.2140.7650.449100
2.96-3.0312.50.66718470.9270.9810.1950.6960.4699.9
3.03-3.111.90.60518680.9180.9790.1820.6320.45899.9
3.1-3.1711.10.52218450.9440.9860.1610.5470.47299.7
3.17-3.2613.30.44618680.9570.9890.1270.4640.52899.9
3.26-3.3613.30.38319020.9690.9920.1090.3990.542100
3.36-3.4613.40.31118440.9780.9940.0880.3240.589100
3.46-3.5913.20.23818640.9870.9970.0680.2480.679100
3.59-3.7313.20.20218630.9890.9970.0580.210.77399.9
3.73-3.912.90.1718850.9910.9980.0490.1770.853100
3.9-4.1111.50.14718770.9910.9980.0450.1540.91299.9
4.11-4.3612.90.12418860.9940.9990.0360.1291.07999.9
4.36-4.713.50.11719070.9950.9990.0330.1221.152100
4.7-5.1713.10.11118910.9940.9980.0320.1151.11499.9
5.17-5.9212.20.10919270.9950.9990.0320.1131.092100
5.92-7.4612.20.09619410.9960.9990.0280.1011.146100
7.46-1011.50.07520590.9980.9990.0230.0781.63899.7

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XEQ

6xeq


Resolution: 2.7404051296→26.8115 Å / SU ML: 0.347134982557 / Cross valid method: FREE R-VALUE / σ(F): 1.38362614579 / Phase error: 24.2417996747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.250957368247 1840 4.90418188118 %
Rwork0.198182406287 35679 -
obs0.20069556817 37519 99.3012730593 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 2.7404051296→26.8115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9845 0 0 123 9968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011452374348510040
X-RAY DIFFRACTIONf_angle_d1.4927479272213606
X-RAY DIFFRACTIONf_chiral_restr0.1552248364941487
X-RAY DIFFRACTIONf_plane_restr0.008090699937321812
X-RAY DIFFRACTIONf_dihedral_angle_d24.80050658913657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7405-2.81440.3270725728851240.2680181123232524X-RAY DIFFRACTION93.042867182
2.8144-2.89710.3727015361461410.2461975746842733X-RAY DIFFRACTION99.8957247132
2.8971-2.99050.3081796801471410.2427532616572717X-RAY DIFFRACTION100
2.9905-3.09730.2879217798821510.2421182321452727X-RAY DIFFRACTION99.8265695456
3.0973-3.22110.2816054536541260.2390787241262734X-RAY DIFFRACTION99.7558423439
3.2211-3.36740.2917152765431530.224523748242710X-RAY DIFFRACTION100
3.3674-3.54460.2411045505361550.1947890658562747X-RAY DIFFRACTION100
3.5446-3.76610.2162487134561420.1827608175732726X-RAY DIFFRACTION99.9651446497
3.7661-4.0560.2551626039921580.1778546392292755X-RAY DIFFRACTION100
4.056-4.46250.2013646492771460.1672589769962772X-RAY DIFFRACTION99.9657416924
4.4625-5.10430.2440456011381290.1779667616792806X-RAY DIFFRACTION99.9659400545
5.1043-6.41630.2692219957981320.2103796234992818X-RAY DIFFRACTION99.7632735881
6.4163-26.81150.2228853951591420.1887376729152910X-RAY DIFFRACTION98.7702265372
Refinement TLS params.Method: refined / Origin x: -9.31204935023 Å / Origin y: 28.1560054068 Å / Origin z: 0.731537714295 Å
111213212223313233
T0.205640429677 Å2-0.0194576579501 Å2-0.0208632874939 Å2-0.398691131481 Å20.0361645724443 Å2--0.338907509045 Å2
L2.81617011722 °2-0.924745662963 °20.0164167104886 °2-2.5325889414 °2-0.507905032789 °2--1.89380942987 °2
S-0.0939182417031 Å °-0.445647642633 Å °-0.139046407824 Å °0.0174891950863 Å °0.11107039261 Å °0.311909748624 Å °0.0144036446252 Å °-0.014550873207 Å °-0.0141996165822 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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