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- PDB-1qhe: ENERGETICS OF A HYDROGEN BOND (CHARGED AND NEUTRAL) AND OF A CATI... -

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Basic information

Entry
Database: PDB / ID: 1qhe
TitleENERGETICS OF A HYDROGEN BOND (CHARGED AND NEUTRAL) AND OF A CATION-PI INTERACTION IN APOFLAVODOXIN
ComponentsPROTEIN (FLAVODOXIN)
KeywordsELECTRON TRANSPORT / FLAVODOXIN
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
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRomero, A. / Fernandez-Recio, J. / Sancho, J.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Energetics of a hydrogen bond (charged and neutral) and of a cation-pi interaction in apoflavodoxin.
Authors: Fernandez-Recio, J. / Romero, A. / Sancho, J.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: STRUCTURE OF APOFLAVODOXIN: CLOSURE OF A TYROSINE/TRYPTOPHAN AROMATIC GATE LEADS TO A COMPACT FOLD
Authors: GENZOR, C.G. / PERALES-ALCON, A. / SANCHO, J. / ROMERO, A.
#2: 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
DepositionMay 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (FLAVODOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8572
Polymers18,7601
Non-polymers961
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.560, 38.600, 62.790
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 PROTEIN (FLAVODOXIN)


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 / Cell line: E.COLI JM109 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / 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.: 90 / 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: 1.8 Å3/Da / Density % sol: 30.7 %
Crystal growpH: 9
Details: 3.2 M AMMONIUM SULPHATE, 0.1 M NA-K PHOSPHATE PH = 9.0. CRYSTALS OF APOFLAVODOXIN APPEARED WITHIN 2 MONTHS.
Crystal
*PLUS
Density % sol: 30.8 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / Details: Genzor, C.G., (1996) Nat.Struct.Biol., 3, 329.
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

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 8777 / % possible obs: 91.8 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.095 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.197 / % possible all: 63.2
Reflection
*PLUS
% possible obs: 95.1 % / Num. measured all: 47838 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 65.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(ROTAVATA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FTG

1ftg


Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 499 -RANDOM
Rwork0.181 ---
obs-8242 91 %-
Displacement parametersBiso mean: 14.52 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 5 90 1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.517
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.79
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.343
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.7
X-RAY DIFFRACTIONx_mcangle_it22.3
X-RAY DIFFRACTIONx_scbond_it22.2
X-RAY DIFFRACTIONx_scangle_it2.52.8
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.306 45 -
Rwork0.243 496 -
obs--65 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSD.PRO
X-RAY DIFFRACTION2PARAM19.SOLAMTOPH19.SO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.79
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.343
X-RAY DIFFRACTIONx_mcbond_it1.51.7
X-RAY DIFFRACTIONx_scbond_it22.2
X-RAY DIFFRACTIONx_mcangle_it22.3
X-RAY DIFFRACTIONx_scangle_it2.52.8
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.243

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