[English] 日本語
Yorodumi
- PDB-2b4t: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b4t
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 Angstrom resolution reveals intriguing extra electron density in the active site
Componentsglyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / GAPDH / GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRobien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 A resolution reveals intriguing extra electron density in the active site
Authors: Robien, M.A. / Bosch, J. / Buckner, F.S. / Van Voorhis, W.C. / Worthey, E.A. / Myler, P. / Mehlin, C. / Boni, E.E. / Kalyuzhniy, O. / Anderson, L. / Lauricella, A. / Gulde, S. / Luft, J.R. / ...Authors: Robien, M.A. / Bosch, J. / Buckner, F.S. / Van Voorhis, W.C. / Worthey, E.A. / Myler, P. / Mehlin, C. / Boni, E.E. / Kalyuzhniy, O. / Anderson, L. / Lauricella, A. / Gulde, S. / Luft, J.R. / Detitta, G. / Caruthers, J.M. / Hodgson, K.O. / Soltis, M. / Zucker, F. / Verlinde, C.L. / Merritt, E.A. / Schoenfeld, L.W. / Hol, W.G.
History
DepositionSep 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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
O: glyceraldehyde-3-phosphate dehydrogenase
P: glyceraldehyde-3-phosphate dehydrogenase
Q: glyceraldehyde-3-phosphate dehydrogenase
R: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,84011
Polymers150,5774
Non-polymers3,2637
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21080 Å2
ΔGint-127 kcal/mol
Surface area44840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.687, 106.056, 91.057
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
glyceraldehyde-3-phosphate dehydrogenase


Mass: 37644.266 Da / Num. of mol.: 4 / Mutation: V3A, N336T, N337S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF14_0598 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)
References: UniProt: Q8T6B1, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 3350; 200 MILLIMOLAR NA F; 100 MILLIMOLAR BIS-TRIS-PROPANE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9807
SYNCHROTRONSSRL BL9-220.9807
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 4, 2005double crystal
QUANTUM 3152CCDMar 4, 2005double crystal
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9807 Å / Relative weight: 1
ReflectionResolution: 2.5→46.625 Å / Num. all: 42843 / Num. obs: 42843 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 68.4 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 6197 / Rsym value: 0.484 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1J0X

1j0x


Resolution: 2.5→43.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 19.138 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21677 2147 5 %RANDOM
Rwork0.17352 ---
all0.17575 40675 --
obs0.17575 40675 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.808 Å2
Baniso -1Baniso -2Baniso -3
1-4.22 Å20 Å21.59 Å2
2---1.07 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10184 0 215 232 10631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210391
X-RAY DIFFRACTIONr_bond_other_d0.0010.029431
X-RAY DIFFRACTIONr_angle_refined_deg1.081.97914169
X-RAY DIFFRACTIONr_angle_other_deg0.712321800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69351328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97324.307397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.659151601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.911543
X-RAY DIFFRACTIONr_chiral_restr0.0590.21645
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022004
X-RAY DIFFRACTIONr_nbd_refined0.1870.22017
X-RAY DIFFRACTIONr_nbd_other0.1690.29657
X-RAY DIFFRACTIONr_nbtor_refined0.1730.25050
X-RAY DIFFRACTIONr_nbtor_other0.080.25994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2412
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.25748476
X-RAY DIFFRACTIONr_mcbond_other0.24942732
X-RAY DIFFRACTIONr_mcangle_it1.647610589
X-RAY DIFFRACTIONr_scbond_it1.92464395
X-RAY DIFFRACTIONr_scangle_it2.797103580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.635 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.389 309 -
Rwork0.322 5882 -
obs--97.59 %
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)
11.78870.1285-0.35851.73880.13811.82520.17670.17350.6462-0.3289-0.0749-0.2672-0.29080.1274-0.1018-0.20820.0406-0.0005-0.10430.08340.134124.18214.887.766
21.1882-0.2843-0.03992.80130.54112.2330.00810.1772-0.2349-0.0407-0.22370.40880.5806-0.23550.2155-0.114-0.045-0.0823-0.0881-0.0994-0.02364.295-17.328.987
32.5014-0.8575-0.46421.77160.23691.0893-0.2186-0.6030.11380.61740.1441-0.35470.33330.29550.07460.06740.0239-0.21920.0988-0.0011-0.056729.795-6.19939.655
41.6133-0.6558-0.1842.11860.44661.4979-0.0123-0.1920.17430.5612-0.130.61940.1506-0.18070.1423-0.1201-0.13310.1113-0.0533-0.14730.1037-5.3698.62635.954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1OA4 - 33612 - 344
2X-RAY DIFFRACTION2PB4 - 33612 - 344
3X-RAY DIFFRACTION3QC4 - 33612 - 344
4X-RAY DIFFRACTION4RD4 - 33612 - 344

+
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