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- PDB-8j3p: Formate dehydrogenase mutant from from Candida dubliniensis M4 co... -

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Basic information

Entry
Database: PDB / ID: 8j3p
TitleFormate dehydrogenase mutant from from Candida dubliniensis M4 complexed with NADP+
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / formate dehydrogenase / complex / 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 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 domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Formate dehydrogenase
Similarity search - Component
Biological speciesCandida dubliniensis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMa, W. / Zheng, Y.C. / Geng, Q. / Chen, C. / Xu, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Chembiochem / Year: 2023
Title: Engineering a Formate Dehydrogenase for NADPH Regeneration.
Authors: Ma, W. / Geng, Q. / Chen, C. / Zheng, Y.C. / Yu, H.L. / Xu, J.H.
History
DepositionApr 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 2.0Oct 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet_range
Item: _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code ..._entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_peptide_omega.omega / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_number_measured_all / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_low / _reflns_shell.number_measured_all / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_chi_squared / _reflns_shell.pdbx_netI_over_sigmaI_obs / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_obs / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Sequence discrepancy / Details: The mistake in T317 was corrected into K317 / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)129,5846
Polymers127,3543
Non-polymers2,2303
Water5,477304
1
A: Formate dehydrogenase
hetero molecules

A: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3894
Polymers84,9022
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8870 Å2
ΔGint-53 kcal/mol
Surface area26800 Å2
MethodPISA
2
B: Formate dehydrogenase
C: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3894
Polymers84,9022
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-50 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.216, 113.022, 401.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 42451.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) (yeast)
Gene: Cd36_53500, CD36_53500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9WHT3, formate dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Chloride, 0.1 M Sodium cacodylate pH 6.5, 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→49.24 Å / Num. obs: 66608 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.021 / Rrim(I) all: 0.073 / Χ2: 1 / Net I/σ(I): 23.9 / Num. measured all: 838613
Reflection shellResolution: 2.3→2.35 Å / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.389 / Num. measured all: 55675 / Num. unique obs: 4450 / CC1/2: 0.974 / Rpim(I) all: 0.114 / Rrim(I) all: 0.405 / Χ2: 0.96 / Net I/σ(I) obs: 6.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.44 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 3401 5.11 %
Rwork0.2304 --
obs0.2331 66492 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8739 0 144 304 9187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.868
X-RAY DIFFRACTIONf_dihedral_angle_d15.4391296
X-RAY DIFFRACTIONf_chiral_restr0.0491371
X-RAY DIFFRACTIONf_plane_restr0.011584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.31171230.29192690X-RAY DIFFRACTION100
2.33-2.370.32711630.28622473X-RAY DIFFRACTION100
2.37-2.40.34741100.29262696X-RAY DIFFRACTION100
2.4-2.440.41271370.29612530X-RAY DIFFRACTION100
2.44-2.490.28651380.28652615X-RAY DIFFRACTION100
2.49-2.530.38671160.31752636X-RAY DIFFRACTION100
2.53-2.580.33551460.30822587X-RAY DIFFRACTION100
2.58-2.630.3581330.29772631X-RAY DIFFRACTION100
2.63-2.690.3349970.31412664X-RAY DIFFRACTION100
2.69-2.750.50991270.32142593X-RAY DIFFRACTION100
2.75-2.820.34071600.29082608X-RAY DIFFRACTION100
2.82-2.90.32921450.2842560X-RAY DIFFRACTION100
2.9-2.980.38391720.27492630X-RAY DIFFRACTION100
2.98-3.080.40241560.26872592X-RAY DIFFRACTION100
3.08-3.190.29031650.26362554X-RAY DIFFRACTION100
3.19-3.320.32611500.25412652X-RAY DIFFRACTION100
3.32-3.470.3581030.2462658X-RAY DIFFRACTION100
3.47-3.650.26281560.22482635X-RAY DIFFRACTION100
3.65-3.880.31691480.21512616X-RAY DIFFRACTION100
3.88-4.180.21231570.18642625X-RAY DIFFRACTION100
4.18-4.60.20271300.16712679X-RAY DIFFRACTION100
4.6-5.260.19971450.16122670X-RAY DIFFRACTION100
5.26-6.620.27411610.19222726X-RAY DIFFRACTION100
6.62-33.440.17681630.17832771X-RAY DIFFRACTION99

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