[English] 日本語
Yorodumi
- PDB-5dn9: Crystal structure of Candida boidinii formate dehydrogenase compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dn9
TitleCrystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide
ComponentsFDH
KeywordsOXIDOREDUCTASE / transition state / ternary complex
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 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 / 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 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 / 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
AZIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase
Similarity search - Component
Biological speciesCandida boidinii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGuo, Q. / Gakhar, L. / Wichersham, K. / Francis, K. / Vardi-Kilshtain, A. / Major, D.T. / Cheatum, C.M. / Kohen, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065368 United States
National Science Foundation (NSF, United States)CHE-1149023 United States
United States - Israel Binational Science Foundation (BSF)2012340 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079368 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.
Authors: Guo, Q. / Gakhar, L. / Wickersham, K. / Francis, K. / Vardi-Kilshtain, A. / Major, D.T. / Cheatum, C.M. / Kohen, A.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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: FDH
B: FDH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2128
Polymers80,7302
Non-polymers1,4826
Water19,5281084
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-66 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.931, 116.617, 63.208
Angle α, β, γ (deg.)90.00, 106.90, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein FDH


Mass: 40364.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida boidinii (fungus) / Gene: FDH
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A1EQY0, formate 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-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1084 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 25% PEG 3000, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 23, 2013
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→41.98 Å / Num. obs: 107639 / % possible obs: 95.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.4 / % possible all: 88.5

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
REFMACrefinement
XDSdata scaling
Cootmodel building
PHASERphasing
Blu-Icedata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6I

2j6i


Resolution: 1.5→41.976 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 15.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1691 10639 4.99 %
Rwork0.1383 --
obs0.1398 107560 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→41.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5636 0 96 1084 6816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095886
X-RAY DIFFRACTIONf_angle_d1.2888003
X-RAY DIFFRACTIONf_dihedral_angle_d13.1592163
X-RAY DIFFRACTIONf_chiral_restr0.073899
X-RAY DIFFRACTIONf_plane_restr0.0071018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4987-1.51580.25552840.24534985X-RAY DIFFRACTION72
1.5158-1.53360.29233330.23996293X-RAY DIFFRACTION89
1.5336-1.55230.2593750.20146622X-RAY DIFFRACTION94
1.5523-1.57190.2233320.18626693X-RAY DIFFRACTION95
1.5719-1.59260.23413900.18896894X-RAY DIFFRACTION96
1.5926-1.61440.21573400.18696677X-RAY DIFFRACTION96
1.6144-1.63750.20563760.17376849X-RAY DIFFRACTION96
1.6375-1.6620.19683620.16956746X-RAY DIFFRACTION96
1.662-1.68790.21143860.16736814X-RAY DIFFRACTION96
1.6879-1.71560.20183350.16346882X-RAY DIFFRACTION96
1.7156-1.74520.17613710.14986795X-RAY DIFFRACTION97
1.7452-1.77690.19183230.14816818X-RAY DIFFRACTION96
1.7769-1.81110.16323310.14586981X-RAY DIFFRACTION97
1.8111-1.84810.18413380.14266808X-RAY DIFFRACTION97
1.8481-1.88830.19953520.14596855X-RAY DIFFRACTION97
1.8883-1.93220.16763590.14416800X-RAY DIFFRACTION97
1.9322-1.98050.18463840.13626918X-RAY DIFFRACTION97
1.9805-2.0340.18663640.14386841X-RAY DIFFRACTION97
2.034-2.09390.17793670.14266890X-RAY DIFFRACTION97
2.0939-2.16150.17243560.13236866X-RAY DIFFRACTION97
2.1615-2.23870.15973830.12596809X-RAY DIFFRACTION97
2.2387-2.32840.16663600.1236897X-RAY DIFFRACTION97
2.3284-2.43430.1513590.12096943X-RAY DIFFRACTION98
2.4343-2.56260.14944020.12066858X-RAY DIFFRACTION98
2.5626-2.72320.16043700.12656895X-RAY DIFFRACTION97
2.7232-2.93340.15613620.13016853X-RAY DIFFRACTION97
2.9334-3.22850.15573280.12666901X-RAY DIFFRACTION97
3.2285-3.69540.13623660.12316775X-RAY DIFFRACTION96
3.6954-4.65490.13543070.11116848X-RAY DIFFRACTION96
4.6549-41.99270.13533440.1286854X-RAY DIFFRACTION97

+
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