[English] 日本語
Yorodumi
- PDB-6t9x: Crystal structure of formate dehydrogenase FDH2 D222Q/Q223R mutan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t9x
TitleCrystal structure of formate dehydrogenase FDH2 D222Q/Q223R mutant enzyme from Granulicella mallensis MP5ACTX8 in complex with NADP and Azide.
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / formate dehydrogenase / NAD / NADP
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 1 / 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
AZIDE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Formate dehydrogenase
Similarity search - Component
Biological speciesGranulicella mallensis MP5ACTX8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRobescu, M.S. / Rubini, R. / Filippini, F. / Bergantino, B. / Cendron, L.
CitationJournal: Chemcatchem / Year: 2020
Title: From the Amelioration of a NADP+-dependent Formate Dehydrogenase to the Discovery of a New Enzyme: Round Trip from Theory to Practice
Authors: Robescu, M.S. / Rubini, R. / Beneventi, E. / Tavanti, M. / Lonigro, C. / Zito, F. / Filippini, F. / Cendron, L. / Bergantino, E.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)173,66812
Polymers170,5274
Non-polymers3,1428
Water13,421745
1
B: Formate dehydrogenase
A: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8346
Polymers85,2632
Non-polymers1,5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-58 kcal/mol
Surface area26130 Å2
MethodPISA
2
C: Formate dehydrogenase
hetero molecules

D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8346
Polymers85,2632
Non-polymers1,5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area10510 Å2
ΔGint-56 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.605, 69.189, 111.841
Angle α, β, γ (deg.)90.000, 93.780, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 275 or resid 277...
21(chain B and (resid 2 through 275 or resid 277...
31(chain C and (resid 2 through 275 or resid 277...
41(chain D and (resid 2 through 275 or resid 277...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYS(chain A and (resid 2 through 275 or resid 277...AB2 - 2752 - 275
12GLYGLYLYSLYS(chain A and (resid 2 through 275 or resid 277...AB277 - 318277 - 318
13HISHISHISHIS(chain A and (resid 2 through 275 or resid 277...AB320320
21ALAALALYSLYS(chain B and (resid 2 through 275 or resid 277...BA2 - 2752 - 275
22GLYGLYLYSLYS(chain B and (resid 2 through 275 or resid 277...BA277 - 318277 - 318
23ALAALAVALVAL(chain B and (resid 2 through 275 or resid 277...BA2 - 3842 - 384
31ALAALALYSLYS(chain C and (resid 2 through 275 or resid 277...CC2 - 2752 - 275
32GLYGLYLYSLYS(chain C and (resid 2 through 275 or resid 277...CC277 - 318277 - 318
33HISHISHISHIS(chain C and (resid 2 through 275 or resid 277...CC320320
41ALAALALYSLYS(chain D and (resid 2 through 275 or resid 277...DD2 - 2752 - 275
42GLYGLYLYSLYS(chain D and (resid 2 through 275 or resid 277...DD277 - 318277 - 318
43ALAALAVALVAL(chain D and (resid 2 through 275 or resid 277...DD2 - 3842 - 384

-
Components

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


Mass: 42631.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Granulicella mallensis MP5ACTX8 (bacteria)
Gene: AciX8_0868 / Production host: Escherichia coli (E. coli) / References: UniProt: G8NTI5, formate dehydrogenase
#2: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 % w/v PEG 1000, 10%w/v PEG8000, 50 mM HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9667 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9667 Å / Relative weight: 1
ReflectionResolution: 2.2→45.751 Å / Num. obs: 430016 / % possible obs: 98.39 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 41605 / % possible all: 98.83

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T8C

6t8c


Resolution: 2.2→45.751 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 7089 4.92 %
Rwork0.1757 136857 -
obs0.1772 74628 97.1 %
all-7439 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.92 Å2 / Biso mean: 26.4641 Å2 / Biso min: 11.4 Å2
Refinement stepCycle: final / Resolution: 2.2→45.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11904 0 204 745 12853
Biso mean--23.92 30.56 -
Num. residues----1532
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7320X-RAY DIFFRACTION8.434TORSIONAL
12B7320X-RAY DIFFRACTION8.434TORSIONAL
13C7320X-RAY DIFFRACTION8.434TORSIONAL
14D7320X-RAY DIFFRACTION8.434TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2250.32041900.2743472398
2.225-2.25120.28122290.2621450297
2.2512-2.27860.27652000.261460797
2.2786-2.30750.29562400.2589460597
2.3075-2.33780.28082380.2579450196
2.3378-2.36990.31462170.2402450696
2.3699-2.40370.25752540.2365443095
2.4037-2.43960.3072360.2374442394
2.4396-2.47770.28482060.2133420991
2.4777-2.51830.23221690.203412587
2.5183-2.56170.2152050.2147420789
2.5617-2.60830.26232710.1981429592
2.6083-2.65850.27332470.1974464998
2.6585-2.71270.2262680.186457199
2.7127-2.77170.2192500.188465199
2.7717-2.83620.20422620.1857464399
2.8362-2.90710.23272390.18034702100
2.9071-2.98570.20692070.1865470499
2.9857-3.07350.24972530.1863463499
3.0735-3.17270.21992200.1856469699
3.1727-3.28610.22972320.182468899
3.2861-3.41760.21842980.1824460399
3.4176-3.57310.18532590.1699464099
3.5731-3.76140.20852640.1577466999
3.7614-3.99690.17392750.148463399
3.9969-4.30530.14972780.126462699
4.3053-4.73820.12372640.1182458299
4.7382-5.42290.13942210.1322469899
5.4229-6.82860.18871930.154472399

+
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