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- PDB-7mya: Structure of proline utilization A with the FAD covalently-modifi... -

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Basic information

Entry
Database: PDB / ID: 7mya
TitleStructure of proline utilization A with the FAD covalently-modified by 1,3-dithiolane
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGNEASE / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding
Similarity search - Function
Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase ...Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / FAD-linked oxidoreductase-like / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-UJJ / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti SM11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.56 Å
AuthorsTanner, J.J. / Campbell, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM132640 United States
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Photoinduced Covalent Irreversible Inactivation of Proline Dehydrogenase by S-Heterocycles.
Authors: Campbell, A.C. / Prater, A.R. / Bogner, A.N. / Quinn, T.P. / Gates, K.S. / Becker, D.F. / Tanner, J.J.
History
DepositionMay 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Aug 3, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.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 / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.pdbx_overall_phase_error / _refine_hist.d_res_low / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns.B_iso_Wilson_estimate / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand geometry
Details: Refined with with improved bond and angle restraints for covalent FDA adduct UJJ.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 18, 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: Bifunctional protein PutA
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,86823
Polymers263,9232
Non-polymers4,94521
Water34,6611924
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A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,17210
Polymers131,9621
Non-polymers2,2109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,69613
Polymers131,9621
Non-polymers2,73512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-115 kcal/mol
Surface area78070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.176, 101.884, 125.931
Angle α, β, γ (deg.)90.000, 106.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional protein PutA


Mass: 131961.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti SM11 (bacteria) / Strain: SM11 / Gene: putA, SM11_chr0102 / Production host: Escherichia coli (E. coli)
References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 8 types, 1945 molecules

#2: Chemical ChemComp-UJJ / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[5-(1,3-dithiolan-2-yl)-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate


Mass: 891.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H39N9O15P2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1924 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein stock solution: 6 mg/mL PutA with 50 mM 1,3-dithiolane-2-carboxylate in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl) ...Details: Protein stock solution: 6 mg/mL PutA with 50 mM 1,3-dithiolane-2-carboxylate in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl)phosphine. Reservoir solution: 19 % PEG-3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M HEPES (pH 8.0), and 0.1 M sodium formate. Cryo-buffer: reservoir supplemented with 15 % PEG-200. Crystals were grown in low-light conditions and then exposed to bright light before flash-cooling to induce the decarboxylation of 1,3-dithiolane-2-carboxylate and covalent modification of the FAD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.56→46.94 Å / Num. obs: 343612 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.054 / Rrim(I) all: 0.103 / Net I/σ(I): 8.7 / Num. measured all: 1229588 / Scaling rejects: 257
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.56-1.593.41.45258494171030.3380.9231.7260.7100
8.54-46.943.60.026769221270.9980.0160.03129.896

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5kf6
Resolution: 1.56→46.94 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 17139 5.01 %
Rwork0.176 324806 -
obs0.1774 341945 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.51 Å2 / Biso mean: 25.8732 Å2 / Biso min: 9.34 Å2
Refinement stepCycle: final / Resolution: 1.56→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17916 0 315 1924 20155
Biso mean--30.81 32.04 -
Num. residues----2434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.580.31825680.3053105411110997
1.58-1.60.32236080.3003106731128197
1.6-1.620.31385630.2897105621112597
1.62-1.640.29795400.2785109501149099
1.64-1.660.30335310.2701109101144199
1.66-1.680.31085560.2816108741143099
1.68-1.70.29315860.2712109141150099
1.7-1.730.28985640.25711093111495100
1.73-1.760.29035360.24531097911515100
1.76-1.790.27625640.2318108971146199
1.79-1.820.26165910.2148108821147399
1.82-1.850.23965420.1985108671140999
1.85-1.890.23056110.1951096511576100
1.89-1.920.24025900.19871088911479100
1.92-1.970.22115760.19141099611572100
1.97-2.010.23865860.19641098511571100
2.01-2.060.23625550.18831088311438100
2.06-2.120.21495770.171098411561100
2.12-2.180.2025540.16451093911493100
2.18-2.250.20595670.1658109281149599
2.25-2.330.1925820.16291085811440100
2.33-2.420.19335930.1607109531154699
2.42-2.530.1985670.1647109131148099
2.53-2.670.20116010.1616108311143299
2.67-2.830.20255710.1704108091138098
2.83-3.050.19195830.167106901127397
3.05-3.360.19156210.1666104861110796
3.36-3.850.17545220.1476103941091694
3.85-4.850.14825750.127104151099094
4.85-46.940.15375590.1497109081146797
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5874-0.01350.19120.1217-0.0120.2151-0.023-0.0362-0.0090.01770.0290.0034-0.0035-0.0092-0.00690.14170.01030.01270.09870.00580.1247-25.885466.126192.6575
20.2223-0.01440.10040.244-0.10270.45410.016-0.0442-0.00950.04220.01810.00140.0433-0.0909-0.03430.11370.00320.00070.1262-0.01170.12085.648631.445691.1032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A')A-1 - 1233
2X-RAY DIFFRACTION2(chain 'B')B-1 - 1233

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