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- PDB-5veg: Structure of a Short-Chain Flavodoxin Associated with a Non-Canon... -

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Basic information

Entry
Database: PDB / ID: 5veg
TitleStructure of a Short-Chain Flavodoxin Associated with a Non-Canonical PDU Bacterial Microcompartment
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / flavodoxin / bacterial microcompartments
Function / homology
Function and homology information


Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / Flavodoxin/nitric oxide synthase / Flavodoxin
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSutter, M. / Plegaria, J.S. / Kerfeld, C.A.
CitationJournal: Biochemistry / Year: 2017
Title: Structural and Functional Characterization of a Short-Chain Flavodoxin Associated with a Noncanonical 1,2-Propanediol Utilization Bacterial Microcompartment.
Authors: Plegaria, J.S. / Sutter, M. / Ferlez, B. / Aussignargues, C. / Niklas, J. / Poluektov, O.G. / Fromwiller, C. / TerAvest, M. / Utschig, L.M. / Tiede, D.M. / Kerfeld, C.A.
History
DepositionApr 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin
B: Flavodoxin
C: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,78715
Polymers57,9433
Non-polymers1,84412
Water3,225179
1
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9064
Polymers19,3141
Non-polymers5923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0195
Polymers19,3141
Non-polymers7044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8636
Polymers19,3141
Non-polymers5485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.301, 95.807, 102.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flavodoxin / / BMC-associated flavodoxin


Mass: 19314.377 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Gene: fldA, A9P83_08720 / Production host: Escherichia coli (E. coli) / References: UniProt: Q50EJ1, UniProt: A5VM92*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 200 mM calcium acetate, 100 mM MES, pH 5.5, 6 mM cadmium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.99→48 Å / Num. obs: 32751 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.3
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.903 / Num. unique obs: 2263 / CC1/2: 0.79 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2650: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5LJL
Resolution: 1.99→47.904 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 2003 6.13 %random selection
Rwork0.2007 ---
obs0.2038 32687 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→47.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 102 179 3702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073574
X-RAY DIFFRACTIONf_angle_d0.8044858
X-RAY DIFFRACTIONf_dihedral_angle_d3.1882081
X-RAY DIFFRACTIONf_chiral_restr0.048547
X-RAY DIFFRACTIONf_plane_restr0.004620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.03980.35351470.2662153X-RAY DIFFRACTION100
2.0398-2.0950.31321340.24172149X-RAY DIFFRACTION100
2.095-2.15660.27721410.22012150X-RAY DIFFRACTION100
2.1566-2.22620.3061460.22722173X-RAY DIFFRACTION100
2.2262-2.30580.28191400.21372141X-RAY DIFFRACTION100
2.3058-2.39810.2621340.2212181X-RAY DIFFRACTION100
2.3981-2.50720.28821460.20562178X-RAY DIFFRACTION100
2.5072-2.63940.27161430.20262177X-RAY DIFFRACTION100
2.6394-2.80480.24121340.20112186X-RAY DIFFRACTION100
2.8048-3.02130.2841510.21312173X-RAY DIFFRACTION100
3.0213-3.32530.26021350.21262206X-RAY DIFFRACTION100
3.3253-3.80630.24541480.17812211X-RAY DIFFRACTION100
3.8063-4.79480.22581490.16922250X-RAY DIFFRACTION100
4.7948-47.91740.20651550.20842356X-RAY DIFFRACTION100

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