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- PDB-1x77: Crystal structure of a NAD(P)H-dependent FMN reductase complexed ... -

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Basic information

Entry
Database: PDB / ID: 1x77
TitleCrystal structure of a NAD(P)H-dependent FMN reductase complexed with FMN
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative (PSI) / FMN reductase / FMN bound / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


FMN reductase (NADPH) activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
: / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NAD(P)H-dependent FMN reductase PA1204
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAgarwal, R. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal.
Authors: Agarwal, R. / Bonanno, J.B. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,1504
Polymers42,2382
Non-polymers9132
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-30 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.473, 65.704, 117.800
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 conserved hypothetical protein


Mass: 21118.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4D4
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.9 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, Calcium acetate, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2004 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 13038 / Num. obs: 13038 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.2
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Num. unique all: 1349 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTT

1rtt


Resolution: 2.7→44.89 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 377503.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The electron density was weak or absent for the missing residues.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 381 3 %RANDOM
Rwork0.219 ---
obs0.219 12497 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7536 Å2 / ksol: 0.332809 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--6.19 Å20 Å2
3----6.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 62 160 2882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.04
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.402 61 3 %
Rwork0.318 1956 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5FMN.PARAMFMN.TOP

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