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- PDB-6t9x: Crystal structure of formate dehydrogenase FDH2 D222Q/Q223R mutan... -

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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 / 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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