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- PDB-3esx: E16KE61KD126KD150K Flavodoxin from Anabaena -

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Basic information

Entry
Database: PDB / ID: 3esx
TitleE16KE61KD126KD150K Flavodoxin from Anabaena
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / ALPHA and BETA PROTEIN / Flavoprotein / FMN / Transport
Function / homology
Function and homology information


cellular response to iron ion starvation / electron transport chain / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / Flavodoxin, conserved site / Flavodoxin signature. / 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
Similarity search - Component
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsHerguedas, B. / Hermoso, J.A. / Martinez-Julvez, M. / Goni, G. / Medina, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Flavodoxin: A compromise between efficiency and versatility in the electron transfer from Photosystem I to Ferredoxin-NADP(+) reductase
Authors: Goni, G. / Herguedas, B. / Hervas, M. / Peregrina, J.R. / De la Rosa, M.A. / Gomez-Moreno, C. / Navarro, J.A. / Hermoso, J.A. / Martinez-Julvez, M. / Medina, M.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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

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Assembly

Deposited unit
A: Flavodoxin
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8208
Polymers37,7522
Non-polymers1,0686
Water4,197233
1
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3723
Polymers18,8761
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4485
Polymers18,8761
Non-polymers5724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.597, 104.142, 37.800
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flavodoxin


Mass: 18875.846 Da / Num. of mol.: 2 / Mutation: E16K, E61K, D126K, D150K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Strain: PCC 7119 / Plasmid: pTrc99a / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P0A3E0
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG 8000, 0.2M Calcium chloride, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Oct 11, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.31→37.76 Å / Num. all: 12191 / Num. obs: 11284 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Rmerge(I) obs: 0.036
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.053 / % possible all: 89.99

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLV

1flv


Resolution: 2.31→18.47 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.87 / SU B: 7.583 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23676 865 7.1 %RANDOM
Rwork0.17608 ---
obs0.18059 11284 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.711 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.31→18.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 66 233 2960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222777
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9723761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4325.797138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40415468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022110
X-RAY DIFFRACTIONr_nbd_refined0.1970.21507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.294
X-RAY DIFFRACTIONr_metal_ion_refined0.3320.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.219
LS refinement shellResolution: 2.311→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 56 -
Rwork0.184 680 -
obs--76.59 %
Refinement TLS params.Method: refined / Origin x: 11.533 Å / Origin y: 12.147 Å / Origin z: 16.173 Å
111213212223313233
T0.0366 Å20.0053 Å20.0023 Å2--0.0323 Å20.0016 Å2---0.0432 Å2
L0.2527 °20.1646 °20.0718 °2-0.1942 °20.0517 °2--0.1036 °2
S-0.0109 Å °-0.0133 Å °0.0066 Å °-0.0115 Å °0.0049 Å °0.0131 Å °0.0048 Å °0.0081 Å °0.0061 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 169
2X-RAY DIFFRACTION1B1 - 169

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