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Entry
Database: PDB / ID: 7btj
TitleCrystal structure of Pennisetum glaucum monodehydroascorbate reductase in complex with FADH2
ComponentsPennisetum glaucum monodehydroascorbate reductase
KeywordsOXIDOREDUCTASE / Nucleotide Binding Oxidoreductase Activity Monodehydroascorbate Reductase (nadh) Activity Flavin Adenine Dinucleotide Binding
Function / homologyDIHYDROFLAVINE-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesCenchrus americanus (bulrush millet)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.373 Å
AuthorsSonkar, K.S. / Achary, M.M. / Reddy, M.K. / Arulandu, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)No.BT/PR18774/BIC/101/454/2016 India
CitationJournal: To Be Published
Title: Crystal structure of Pennisetum glaucum monodehydroascorbate reductase
Authors: Sonkar, K.S. / Arulandu, A. / Achary, M.M. / Reddy, M.K.
History
DepositionApr 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 2.0Sep 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / citation_author / database_2 / entity / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / refine / refine_analyze / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conf / struct_mon_prot_cis / struct_sheet_range / struct_site / struct_site_gen
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_contact_author.id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _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 / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_R_Cruickshank_DPI / _refine.pdbx_overall_SU_R_Blow_DPI / _refine.pdbx_overall_SU_R_free_Blow_DPI / _refine.pdbx_overall_SU_R_free_Cruickshank_DPI / _refine_analyze.Luzzati_coordinate_error_obs / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _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 / _refine_ls_shell.d_res_high / _reflns.number_obs / _reflns_shell.number_unique_obs / _struct.title / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _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: Ligand identity
Details: FAD is replaced with FADH2 in all four chains (A,B,C and D). We have confirmed this through spectroscopic analysis.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pennisetum glaucum monodehydroascorbate reductase
B: Pennisetum glaucum monodehydroascorbate reductase
C: Pennisetum glaucum monodehydroascorbate reductase
D: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,17612
Polymers187,3734
Non-polymers5,8048
Water9,962553
1
A: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2943
Polymers46,8431
Non-polymers1,4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area17800 Å2
MethodPISA
2
B: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2943
Polymers46,8431
Non-polymers1,4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-5 kcal/mol
Surface area17770 Å2
MethodPISA
3
C: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2943
Polymers46,8431
Non-polymers1,4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area17740 Å2
MethodPISA
4
D: Pennisetum glaucum monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2943
Polymers46,8431
Non-polymers1,4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-6 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.730, 79.118, 90.687
Angle α, β, γ (deg.)96.390, 97.270, 111.920
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pennisetum glaucum monodehydroascorbate reductase


Mass: 46843.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cenchrus americanus (bulrush millet) / Gene: MDHAR / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: monodehydroascorbate reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.19 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate pH 6.5 30% w/v Polyethylene glycol 8,000
PH range: 6.4 - 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.37→61.45 Å / Num. obs: 64802 / % possible obs: 96.6 % / Redundancy: 4.9 % / CC1/2: 0.997 / Net I/σ(I): 2.21
Reflection shellResolution: 2.373→2.413 Å / Num. unique obs: 15670 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (11-DEC-2020)refinement
PDB_EXTRACT3.25data extraction
ARP/wARP7.6model building
BALBES1.0.0phasing
PHENIX1.15-3459-000model building
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JCI

5jci


Resolution: 2.373→61.45 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.532 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.488 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 3231 4.99 %RANDOM
Rwork0.1857 ---
obs0.1886 64801 96.6 %-
Displacement parametersBiso max: 92.79 Å2 / Biso mean: 41.01 Å2 / Biso min: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1-5.5957 Å22.761 Å2-5.1746 Å2
2--5.9714 Å2-1.7536 Å2
3----11.5671 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.373→61.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12847 0 388 553 13788
Biso mean--34.41 36.88 -
Num. residues----1728
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4467SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2483HARMONIC5
X-RAY DIFFRACTIONt_it13557HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1793SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11647SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13557HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg18480HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion16.88
LS refinement shellResolution: 2.39→2.39 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3305 75 5.78 %
Rwork0.2701 1222 -
obs--94.69 %

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