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- PDB-4e5p: Thermostable phosphite dehydrogenase A176R variant in complex with NAD -

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Basic information

Entry
Database: PDB / ID: 4e5p
TitleThermostable phosphite dehydrogenase A176R variant in complex with NAD
ComponentsThermostable phosphite dehydrogenase A176R variant
KeywordsOXIDOREDUCTASE / D-2-hydroxyacid dehydrogenase
Function / homology
Function and homology information


phosphonate dehydrogenase / phosphonate dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Phosphonate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZou, Y. / Zhang, H. / Nair, S.K.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration.
Authors: Zou, Y. / Zhang, H. / Brunzelle, J.S. / Johannes, T.W. / Woodyer, R. / Hung, J.E. / Nair, N. / van der Donk, W.A. / Zhao, H. / Nair, S.K.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermostable phosphite dehydrogenase A176R variant
B: Thermostable phosphite dehydrogenase A176R variant
C: Thermostable phosphite dehydrogenase A176R variant
D: Thermostable phosphite dehydrogenase A176R variant
E: Thermostable phosphite dehydrogenase A176R variant
F: Thermostable phosphite dehydrogenase A176R variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,49712
Polymers217,5166
Non-polymers3,9816
Water24,1041338
1
A: Thermostable phosphite dehydrogenase A176R variant
C: Thermostable phosphite dehydrogenase A176R variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8324
Polymers72,5052
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-49 kcal/mol
Surface area25820 Å2
MethodPISA
2
B: Thermostable phosphite dehydrogenase A176R variant
D: Thermostable phosphite dehydrogenase A176R variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8324
Polymers72,5052
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-46 kcal/mol
Surface area25610 Å2
MethodPISA
3
E: Thermostable phosphite dehydrogenase A176R variant
F: Thermostable phosphite dehydrogenase A176R variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8324
Polymers72,5052
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-53 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.298, 122.263, 134.322
Angle α, β, γ (deg.)90.00, 96.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thermostable phosphite dehydrogenase A176R variant


Mass: 36252.727 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69054*PLUS
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1338 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25-30% PEG 3350, 100 mM KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 171899 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.5 / % possible all: 89.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0056refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Thermostable phosphite dehydrogenase E175A variant

Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.085 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24138 8567 5 %RANDOM
Rwork0.19953 ---
obs0.20161 163207 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.666 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å23.83 Å2
2---1.94 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15076 0 264 1338 16678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02215643
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.98721325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35951963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86623.107708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.231152469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.17615160
X-RAY DIFFRACTIONr_chiral_restr0.0760.22471
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111900
X-RAY DIFFRACTIONr_gen_planes_other0.0210.0214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5391.59788
X-RAY DIFFRACTIONr_mcbond_other0.081.510
X-RAY DIFFRACTIONr_mcangle_it1.036215614
X-RAY DIFFRACTIONr_scbond_it1.64235855
X-RAY DIFFRACTIONr_scangle_it2.7264.55711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 580 -
Rwork0.29 10131 -
obs--82.51 %

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