[English] 日本語
Yorodumi
- PDB-7btj: Crystal structure of Pennisetum glaucum monodehydroascorbate redu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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) (unknown) / 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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more