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- PDB-1ftg: STRUCTURE OF APOFLAVODOXIN: CLOSURE OF A TYROSINE/TRYPTOPHAN AROM... -

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Basic information

Entry
Database: PDB / ID: 1ftg
TitleSTRUCTURE OF APOFLAVODOXIN: CLOSURE OF A TYROSINE/TRYPTOPHAN AROMATIC GATE LEADS TO A COMPACT FOLD
ComponentsAPOFLAVODOXIN
KeywordsELECTRON 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 ...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
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRomero, A.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Closure of a tyrosine/tryptophan aromatic gate leads to a compact fold in apo flavodoxin.
Authors: Genzor, C.G. / Perales-Alcon, A. / Sancho, J. / Romero, A.
#1: Journal: Protein Sci. / Year: 1992
Title: Structure of the Oxidized Long-Chain Flavodoxin from Anabaena 7120 at 2 A Resolution
Authors: Rao, S.T. / Shaffie, F. / Yu, C. / Satyshur, K.A. / Stockman, B.J. / Markley, J.L. / Sundarlingam, M.
History
DepositionNov 21, 1995Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOFLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8572
Polymers18,7601
Non-polymers961
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.480, 38.600, 60.270
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 APOFLAVODOXIN


Mass: 18760.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7119 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3E0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 28.49 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-12 mg/mlprotein1drop
250 mMTris-HCl1drop
33.2 Mammonium sulfate1reservoir
40.1 Msodium potassium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Aug 25, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 8437 / % possible obs: 92 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.074
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 9999 Å / Num. measured all: 56317

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.182 -
obs0.182 7823
Displacement parametersBiso mean: 16.22 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 5 94 1425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.482
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_deg1.371

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