[English] 日本語
Yorodumi
- PDB-1psd: THE ALLOSTERIC LIGAND SITE IN THE VMAX-TYPE COOPERATIVE ENZYME PH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1psd
TitleTHE ALLOSTERIC LIGAND SITE IN THE VMAX-TYPE COOPERATIVE ENZYME PHOSPHOGLYCERATE DEHYDROGENASE
ComponentsD-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE (NAD(A))
Function / homology
Function and homology information


2-hydroxyglutarate dehydrogenase activity / 2-oxoglutarate reductase / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / serine binding / NADH binding / L-serine biosynthetic process / NAD+ binding / identical protein binding / cytosol
Similarity search - Function
ACT domain / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / ACT domain profile. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain ...ACT domain / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / ACT domain profile. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / ACT-like domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SERINE / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsSchuller, D.J. / Grant, G.A. / Banaszak, L.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.
Authors: Schuller, D.J. / Grant, G.A. / Banaszak, L.J.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Enhanced Expression of the Escherichia Coli Sera Gene in a Plasmid Vector: Purification, Crystallization, and Preliminary X-Ray Dat of D-3-Phosphoglycerate Dehydrogenase
Authors: Schuller, D.J. / Fetter, C.H. / Banaszak, L.J. / Grant, G.A.
#2: Journal: J.Biol.Chem. / Year: 1986
Title: The Nucleotide Sequence of the Sera Gene of Escherichia Coli and the Amino Acid Sequence of the Encoded Protein, D-3-Phosphoglycerate Dehydrogenase
Authors: Tobey, K.L. / Grant, G.A.
History
DepositionMay 2, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET BETA SHEET RA FROM SUBUNIT A ALIGNS WITH BETA SHEET RB OF SUBUNIT B TO FORM AN 8 STRAND SHEET. ...SHEET BETA SHEET RA FROM SUBUNIT A ALIGNS WITH BETA SHEET RB OF SUBUNIT B TO FORM AN 8 STRAND SHEET. STRAND R-4 OF ONE SUBUNIT CONTACTS STRAND R-4 OF THE OTHER. REGISTER: ASN 368 O - LEU 370 N, ASN 368 N - LEU 370 O.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)
B: D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7286
Polymers88,1912
Non-polymers1,5374
Water1,36976
1
A: D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)
B: D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)
hetero molecules

A: D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)
B: D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,45612
Polymers176,3824
Non-polymers3,0748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area18920 Å2
ΔGint-83 kcal/mol
Surface area62380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.100, 146.300, 53.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7139, -0.6964, 0.07357), (-0.6949, 0.69129, -0.1965), (0.08612, -0.1913, -0.9774)115.3736, 54.98566, 67.00005
2given(-0.7583, -0.65189, 0.00034), (-0.65184, 0.7582, -0.01316), (0.00884, -0.0098, -0.9999)118.25562, 47.1008, 68.99728
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 108 .. 294 B 109 .. 294 0.383 M2 A 7 .. 107 B 7 .. 107 0.680 M2 A 295 .. 336 B 295 .. 336 0.692 M2 A 337 .. 410 B 337 .. 410 0.622 SUBUNITS A AND B IN THIS ENTRY FORM A TETRAMER WITH SUBUNITS A' AND B' WHICH CAN BE GENERATED BY APPLYING THE FOLLOWING CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATION TO THE COORDINATES IN THIS ENTRY: -1.0 0.0 0.0 136.1 0.0 -1.0 0.0 0.0 0.0 0.0 1.0 0.0

-
Components

#1: Protein D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)


Mass: 44095.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Strain (production host): K12 / References: UniProt: P0A9T0, phosphoglycerate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES A 258, A 260, A 263 AND B 258, B 260, B 263 ARE THE GLYCINES OF GXGXXG NUCLEOTIDE BINDING ...RESIDUES A 258, A 260, A 263 AND B 258, B 260, B 263 ARE THE GLYCINES OF GXGXXG NUCLEOTIDE BINDING CONSENSUS. A 269, B 269 GLUTAMIC ACID PAIRED WITH 292 IN 'PROTON SHUTTLE'. A 292, B 292 PRESUMED CATALYTIC HISTIDINE.
Nonpolymer detailsC 451, D 451 ALLOSTERIC LIGAND SERINE; NOT PART OF POLYPEPTIDE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1400 mMsodium citrate1reservoir
214 %PEG33501reservoir
310 mg/mlPGDH1drop
44 mMserine1drop
54 mMNAD1drop
62 mMDTT1drop
71 mMEDTA1drop
80.05 %sodium azide1drop
9400 mMsodium citrate1drop
1014 %PEG33501drop

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 26417 / % possible obs: 84 %
Reflection
*PLUS
Num. measured all: 287548 / Rmerge(I) obs: 0.119

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.75→9 Å / σ(F): 2
Details: RESIDUES A 114 AND B 114 WERE MISTAKENLY REFINED AS ASP; BUT SHOULD BE GLU. GLU HAS BEEN SUBSTITUTED BUT NOT REFINED.
RfactorNum. reflection
Rwork0.177 -
obs0.177 21295
Refinement stepCycle: LAST / Resolution: 2.75→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 102 76 6304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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