[English] 日本語
Yorodumi
- PDB-5izd: Wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5izd
TitleWild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP
ComponentsD-glyceraldehyde dehydrogenase (NADP(+))
KeywordsOXIDOREDUCTASE / NADP-dependent dehydrogenase
Function / homology
Function and homology information


D-glyceraldehyde dehydrogenase (NADP+) / glyceraldehyde dehydrogenase (NADP+) activity / Entner-Doudoroff pathway through 6-phosphogluconate / glycolytic process / protein homotetramerization / protein homodimerization activity
Similarity search - Function
: / : / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...: / : / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / D-glyceraldehyde dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsIermak, I. / Mesters, J.R. / Kuta Smatanova, I.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of SciencesDAAD-16-09 Czech Republic
CitationJournal: To Be Published
Title: Structure of wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP
Authors: Iermak, I. / Mesters, J.R. / Steffler, F. / Sieber, V. / Kuta Smatanova, I.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Data collection
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-glyceraldehyde dehydrogenase (NADP(+))
B: D-glyceraldehyde dehydrogenase (NADP(+))
C: D-glyceraldehyde dehydrogenase (NADP(+))
D: D-glyceraldehyde dehydrogenase (NADP(+))
E: D-glyceraldehyde dehydrogenase (NADP(+))
F: D-glyceraldehyde dehydrogenase (NADP(+))
G: D-glyceraldehyde dehydrogenase (NADP(+))
H: D-glyceraldehyde dehydrogenase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)456,85214
Polymers452,3928
Non-polymers4,4606
Water24,3741353
1
A: D-glyceraldehyde dehydrogenase (NADP(+))
B: D-glyceraldehyde dehydrogenase (NADP(+))
C: D-glyceraldehyde dehydrogenase (NADP(+))
D: D-glyceraldehyde dehydrogenase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,1708
Polymers226,1964
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27020 Å2
ΔGint-121 kcal/mol
Surface area57910 Å2
MethodPISA
2
E: D-glyceraldehyde dehydrogenase (NADP(+))
F: D-glyceraldehyde dehydrogenase (NADP(+))
G: D-glyceraldehyde dehydrogenase (NADP(+))
H: D-glyceraldehyde dehydrogenase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,6836
Polymers226,1964
Non-polymers1,4872
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25620 Å2
ΔGint-114 kcal/mol
Surface area58300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.289, 152.353, 149.905
Angle α, β, γ (deg.)90.00, 92.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
D-glyceraldehyde dehydrogenase (NADP(+)) / Glyceraldehyde DH


Mass: 56548.973 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0809 / Plasmid: pCBRHisC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HK01, D-glyceraldehyde dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1353 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM glutamic acid (racemic), 20 mM glycine, 20 mM serine (racemic), 20 mM alanine (racemic), 20 mM lysine-HCl (racemic), 50 mM MOPS, 50 mM Sodium HEPES, pH 7.5; 20% Ethylene Glycol, 10% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.95→48.1 Å / Num. obs: 310836 / % possible obs: 99.8 % / Redundancy: 6.84 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.38
Reflection shellResolution: 1.95→2.06 Å / Mean I/σ(I) obs: 1.98 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSNovember 3, 2014data reduction
BALBES1.0.0.Nov_16_2011phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2W

3k2w


Resolution: 2.05→48.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.283 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 13347 5 %RANDOM
Rwork0.16838 ---
obs0.17021 253577 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.134 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å2-0 Å2-1.04 Å2
2---2.5 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30004 0 186 1353 31543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01930948
X-RAY DIFFRACTIONr_bond_other_d0.0020.0228847
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.94942004
X-RAY DIFFRACTIONr_angle_other_deg1.032.99766267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31453932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76324.3531321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.529155017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.73515154
X-RAY DIFFRACTIONr_chiral_restr0.1030.24587
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02135310
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027002
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_it0.4390.90615710
X-RAY DIFFRACTIONr_mcbond_other0.4390.90615709
X-RAY DIFFRACTIONr_mcangle_it0.7531.35619624
X-RAY DIFFRACTIONr_mcangle_other0.7531.35619625
X-RAY DIFFRACTIONr_scbond_it0.730.99415238
X-RAY DIFFRACTIONr_scbond_other0.7220.99115230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1631.46622360
X-RAY DIFFRACTIONr_long_range_B_refined6.0928.22535742
X-RAY DIFFRACTIONr_long_range_B_other6.0617.77235185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 982 -
Rwork0.236 18671 -
obs--99.98 %
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)
10.72710.00220.40830.3314-0.05130.69150.01660.01470.0387-0.02160.00220.0418-0.09440.0977-0.01880.0544-0.01780.01180.3641-0.02860.3139-13.6067.1726.941
20.5666-0.01510.09060.4713-0.11210.5690.0895-0.0426-0.2077-0.06210.02760.20250.1801-0.0356-0.11710.1074-0.0205-0.10660.37220.03510.5215-34.875-25.6458.494
30.5480.2069-0.08470.4922-0.06860.52450.0205-0.1217-0.0540.1323-0.0849-0.0996-0.02950.08470.06450.0491-0.01350.0020.33760.03380.281538.691-7.749101.382
40.57010.2402-0.23140.6836-0.20280.6303-0.09780.1496-0.062-0.06670.05960.00740.0108-0.13220.03820.0249-0.01770.04260.3518-0.02450.259417.781-9.53268.031
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 494
2X-RAY DIFFRACTION1B1 - 492
3X-RAY DIFFRACTION1A601
4X-RAY DIFFRACTION1B601
5X-RAY DIFFRACTION2C1 - 492
6X-RAY DIFFRACTION2D1 - 492
7X-RAY DIFFRACTION2C601
8X-RAY DIFFRACTION2D601
9X-RAY DIFFRACTION3E1 - 492
10X-RAY DIFFRACTION3F1 - 492
11X-RAY DIFFRACTION4G1 - 492
12X-RAY DIFFRACTION4H1 - 492
13X-RAY DIFFRACTION4H601
14X-RAY DIFFRACTION4G601

+
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