[English] 日本語
Yorodumi
- PDB-2nac: HIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nac
TitleHIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE
ComponentsNAD-DEPENDENT FORMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(ALDEHYDE(D) / NAD+(A))
Function / homology
Function and homology information


formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytoplasm
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain ...NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic 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 / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Formate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLamzin, V.S. / Dauter, Z. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: High resolution structures of holo and apo formate dehydrogenase.
Authors: Lamzin, V.S. / Dauter, Z. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S.
#1: Journal: Eur.J.Biochem. / Year: 1992
Title: Crystal Structure of Nad-Dependent Formate Dehydrogenase
Authors: Lamzin, V.S. / Aleshin, A.E. / Strokopytov, B.V. / Yukhnevich, M.G. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S.
History
DepositionJul 6, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-DEPENDENT FORMATE DEHYDROGENASE
B: NAD-DEPENDENT FORMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7664
Polymers86,5742
Non-polymers1922
Water15,547863
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-71 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.460, 54.470, 70.290
Angle α, β, γ (deg.)90.00, 101.91, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 312 / 2: CIS PROLINE - PRO A 314 / 3: CIS PROLINE - PRO B 312 / 4: CIS PROLINE - PRO B 314
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.53022, -0.52775, -0.66359), (-0.51793, -0.82127, 0.23931), (-0.67128, 0.2168, -0.70878)
Vector: 46.367, 33.648, 80.094)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

-
Components

#1: Protein NAD-DEPENDENT FORMATE DEHYDROGENASE


Mass: 43286.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: 101 / References: UniProt: P33160, formate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 863 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: FDH_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: FDH_PSESR SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE SER 77 ASP A 77 VAL 138 THR A 138 THR 139 VAL A 139 VAL 145 CYS A 145 HIS 215 VAL A 215 VAL 216 HIS A 216 ASP 327 ASN A 327 SER 77 ASP B 77 VAL 138 THR B 138 THR 139 VAL B 139 VAL 145 CYS B 145 HIS 215 VAL B 215 VAL 216 HIS B 216 ASP 327 ASN B 327 THE GENE SEQUENCE OF THE PSEUDOMONAS SP. 101 FORMATE DEHYDROGENASE IS ALSO AVAILABLE (TISHKOV ET AL., 1991, DOKL. ACAD. NAUK USSR (USSR), 317, 745 - 748), WHICH AGREES WITH THE COORDINATE SET. THIS HAS BEEN DISCUSSED IN THE PAPER CITED ON JRNL RECORDS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
145 %satammonium sulfate1reservoirprecipitant
25 %MPD1reservoir
35 mMNAD1reservoir
45 mMsodium azide1reservoir

-
Data collection

Reflection
*PLUS
Num. obs: 61933 / % possible obs: 89.7 % / Observed criterion σ(I): 3 / Num. measured all: 308786 / Rmerge(I) obs: 0.058 / Biso Wilson estimate: 13.9 Å2
Reflection shell
*PLUS
% possible obs: 69.3 % / Rmerge(I) obs: 0.129

-
Processing

Software
NameClassification
ARP/wARPmodel building
PROLSQrefinement
RefinementResolution: 1.8→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.146 73563
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5840 0 10 863 6713
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.643
X-RAY DIFFRACTIONp_mcangle_it3.634
X-RAY DIFFRACTIONp_scbond_it6.075
X-RAY DIFFRACTIONp_scangle_it8.826
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.1760.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2220.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.093
X-RAY DIFFRACTIONp_staggered_tor15.4115
X-RAY DIFFRACTIONp_orthonormal_tor32.9620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/ARP / Classification: refinement
Refinement
*PLUS
Num. reflection all: 73563 / Rfactor all: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.7 Å2

+
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