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- PDB-1i0s: ARCHAEOGLOBUS FULGIDUS FERRIC REDUCTASE COMPLEX WITH NADP+ -

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Basic information

Entry
Database: PDB / ID: 1i0s
TitleARCHAEOGLOBUS FULGIDUS FERRIC REDUCTASE COMPLEX WITH NADP+
ComponentsCONSERVED HYPOTHETICAL PROTEIN
KeywordsOXIDOREDUCTASE / six stranded antiparallel beta-barrel / FMN and NADP+ binding domain
Function / homology
Function and homology information


ferric-chelate reductase [NAD(P)H] / ferric-chelate reductase (NADH) activity / oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor / ferric-chelate reductase (NADPH) activity / riboflavin reductase (NADPH) activity / FMN binding / protein homodimerization activity
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferric-chelate reductase (NAD(P)H)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChiu, H.-J. / Johnson, E. / Schroder, I. / Rees, D.C.
CitationJournal: Structure / Year: 2001
Title: Crystal structures of a novel ferric reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus and its complex with NADP+.
Authors: Chiu, H.J. / Johnson, E. / Schroder, I. / Rees, D.C.
History
DepositionJan 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Aug 9, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CONSERVED HYPOTHETICAL PROTEIN
B: CONSERVED HYPOTHETICAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5664
Polymers37,3672
Non-polymers1,2002
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-44 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.047, 56.047, 212.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CONSERVED HYPOTHETICAL PROTEIN / FERRIC REDUCTASE


Mass: 18683.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: AF0830 / Production host: Escherichia coli (E. coli) / References: UniProt: O29428
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG4000, SODIUM ACETATE, TRIS-HCL, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
20.1 MTris-HCl1drop
321-22 %(w/v)PEG40001reservoir
40.1 Msodium acetate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 20, 1999 / Details: MIRRORS
RadiationMonochromator: CYCLINDRICALLY BENT CUBED ROOT SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 36289 / Num. obs: 35546 / % possible obs: 0.846 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.204 / % possible all: 86.5
Reflection
*PLUS
% possible obs: 86.1 % / Num. measured all: 168005
Reflection shell
*PLUS
% possible obs: 86.5 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I0R

1i0r


Resolution: 1.65→20 Å / Data cutoff high rms absF: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1763 5 %RANDOM
Rwork0.1908 ---
all0.1915 36289 --
obs0.1915 35546 84.6 %-
Displacement parametersBiso mean: 19.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.206 Å0.1798 Å
Luzzati d res low-20 Å
Luzzati sigma a0.116 Å0.0646 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 79 237 2859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.421
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.57
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.888
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1231.5
X-RAY DIFFRACTIONc_mcangle_it1.8522
X-RAY DIFFRACTIONc_scbond_it1.8152
X-RAY DIFFRACTIONc_scangle_it2.7322.5
Xplor fileSerial no: 1 / Param file: FMN.PAR / Topol file: FMN.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.57
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.888

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