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- PDB-7ya3: Formate dehydrogenase from Novosphingobium sp. AP12 with NADP and... -

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Basic information

Entry
Database: PDB / ID: 7ya3
TitleFormate dehydrogenase from Novosphingobium sp. AP12 with NADP and Azide
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 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 speciesNovosphingobium sp. AP12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,6206
Polymers87,0492
Non-polymers1,5714
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-48 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.343, 64.343, 180.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 43524.391 Da / Num. of mol.: 2
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, EC: 1.17.1.10
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium malonate

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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 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14557 / % possible obs: 99.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.047 / Rrim(I) all: 0.1 / Χ2: 3.097 / Net I/σ(I): 13.5 / Num. measured all: 59350
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.053.40.3057250.8550.1840.3581.49698.6
3.05-3.113.50.2786800.870.1660.3261.68397.3
3.11-3.173.50.2367350.9170.140.2761.64398.7
3.17-3.233.70.227300.940.1260.2551.70498.9
3.23-3.33.90.1797180.9570.10.2051.89699.6
3.3-3.3840.1657470.9640.0910.1892.14299.2
3.38-3.4640.1476970.9730.0810.1682.19499.3
3.46-3.564.20.1297480.9810.0690.1472.27799.2
3.56-3.664.40.1377120.9780.070.1543.65299.9
3.66-3.784.50.1427760.9790.0710.1595.50799.7
3.78-3.914.30.0946990.990.0490.1072.78299.7
3.91-4.074.10.097280.9910.0470.1023.03999.2
4.07-4.264.10.0797360.9930.0420.093.1999.7
4.26-4.484.40.0947130.9890.0480.1066.40899.6
4.48-4.7640.0667320.9930.0350.0753.18299.5
4.76-5.134.20.0687450.9930.0360.0773.10399.7
5.13-5.644.20.0717310.9930.0370.082.86299.2
5.64-6.464.40.0677370.9940.0350.0762.91699.6
6.46-8.134.50.0567380.9960.0290.0633.09399.7
8.13-504.10.0567300.9930.0310.0645.0996.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6t9w

6t9w


Resolution: 3→30.32 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.885 / SU B: 20.721 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 704 4.8 %RANDOM
Rwork0.1673 ---
obs0.1715 13839 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.03 Å2 / Biso mean: 65.903 Å2 / Biso min: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å2-0 Å20 Å2
2--1.12 Å20 Å2
3----2.24 Å2
Refinement stepCycle: final / Resolution: 3→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5947 0 102 2 6051
Biso mean--58.36 27.02 -
Num. residues----766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126207
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165602
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.6438447
X-RAY DIFFRACTIONr_angle_other_deg0.4561.55513069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3425764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.5711036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.743101001
X-RAY DIFFRACTIONr_chiral_restr0.0590.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021198
LS refinement shellResolution: 3→3.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 44 -
Rwork0.261 984 -
all-1028 -
obs--95.72 %

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