[English] 日本語
Yorodumi
- PDB-7ya4: Formate dehydrogenase from Novosphingobium sp. AP12 with NAD and Azide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ya4
TitleFormate dehydrogenase from Novosphingobium sp. AP12 with NAD and Azide
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / Formate dehydrogenase / Complex / NAD
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 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 domain superfamily
Similarity search - Domain/homology
ACETATE ION / AZIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase
Similarity search - Component
Biological speciesNovosphingobium sp. AP12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, S. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning (MSIP)2021M3D3A1A01079480_2021-5 Korea, Republic Of
CitationJournal: To Be Published
Title: Dual cofactor specific formate dehydrogenase from Novosphingobium sp. AP12 with high activity.
Authors: Kim, S. / Kim, K.-J.
History
DepositionJun 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formate dehydrogenase
B: Formate dehydrogenase
C: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,14517
Polymers174,0984
Non-polymers2,04813
Water17,384965
1
A: Formate dehydrogenase
C: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,14810
Polymers87,0492
Non-polymers1,0998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-39 kcal/mol
Surface area27740 Å2
MethodPISA
2
B: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9977
Polymers87,0492
Non-polymers9495
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-49 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.794, 95.789, 117.930
Angle α, β, γ (deg.)90.000, 99.282, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Formate dehydrogenase / / FDH / NAD-dependent formate dehydrogenase


Mass: 43524.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His-tag: LEHHHHHH (385-392) / Source: (gene. exp.) Novosphingobium sp. AP12 (bacteria) / Gene: PMI02_01157 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: J2HCX1, formate dehydrogenase

-
Non-polymers , 7 types, 978 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 965 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tacsimate (Hampton Research, USA)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 143534 / % possible obs: 97.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.6
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.287 / Num. unique obs: 6878

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XYB

4xyb


Resolution: 1.8→34.138 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.5 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1908 7007 4.988 %
Rwork0.1552 133479 -
all0.157 --
obs-140486 97.707 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.855 Å2-0 Å2-1.96 Å2
2--1.168 Å20 Å2
3----1.312 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11796 0 135 965 12896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01212231
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611110
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.64116612
X-RAY DIFFRACTIONr_angle_other_deg0.5271.55525920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13651513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.7771072
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.134101994
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.15410530
X-RAY DIFFRACTIONr_chiral_restr0.0780.21810
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022350
X-RAY DIFFRACTIONr_nbd_refined0.2190.22341
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.210387
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25901
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2774
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.219
X-RAY DIFFRACTIONr_nbd_other0.1680.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.219
X-RAY DIFFRACTIONr_mcbond_it1.3461.7056065
X-RAY DIFFRACTIONr_mcbond_other1.3381.7046064
X-RAY DIFFRACTIONr_mcangle_it1.8262.557573
X-RAY DIFFRACTIONr_mcangle_other1.8262.557574
X-RAY DIFFRACTIONr_scbond_it2.2471.9496166
X-RAY DIFFRACTIONr_scbond_other2.2471.9496167
X-RAY DIFFRACTIONr_scangle_it3.5022.8139039
X-RAY DIFFRACTIONr_scangle_other3.5022.8139040
X-RAY DIFFRACTIONr_lrange_it4.20724.8513747
X-RAY DIFFRACTIONr_lrange_other4.1724.45613540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.2434830.21394300.214105410.9530.96694.04230.177
1.847-1.8970.2415140.20194670.203103240.9590.97196.67760.166
1.897-1.9520.214710.18592430.186100190.9690.97696.95580.153
1.952-2.0120.2214560.17989810.18197060.9650.97997.22850.151
2.012-2.0770.2064630.16587940.16794620.9730.98297.83340.14
2.077-2.150.2184730.16484930.16791300.970.98398.20370.144
2.15-2.2310.2044440.15281840.15488130.9730.98597.90080.134
2.231-2.3220.1984030.1578600.15284660.9760.98697.60220.131
2.322-2.4240.1924110.14676010.14881730.9780.98798.03010.13
2.424-2.5420.1863790.14272410.14577780.9790.98897.96860.128
2.542-2.6790.2033460.14568940.14773970.9770.98797.87750.132
2.679-2.840.183410.14765850.14970570.980.98798.14370.138
2.84-3.0350.1963260.15861530.1665840.9770.98598.40520.15
3.035-3.2760.1893160.16457830.16561550.9780.98499.09020.161
3.276-3.5850.1982710.16353790.16556870.9790.98699.34940.165
3.585-4.0030.1722680.1548620.15151540.9840.98899.53430.155
4.003-4.6110.1442330.12442940.12545540.9890.99299.40710.135
4.611-5.6220.1441770.13536790.13638920.9890.99199.0750.15
5.622-7.8450.1751470.14428780.14630320.9850.9999.76910.159
7.845-34.1380.194850.14716780.14917850.9860.9998.76750.18

+
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