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- PDB-3g59: Crystal Structure of Candida glabrata FMN Adenylyltransferase in ... -

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Basic information

Entry
Database: PDB / ID: 3g59
TitleCrystal Structure of Candida glabrata FMN Adenylyltransferase in complex with ATP
ComponentsFMN Adenylyltransferase
KeywordsTRANSFERASE / FAD biosynthesis / alpha/beta protein / Rossmann-like fold / ATP binding / extended loop region
Function / homology
Function and homology information


FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / PYROPHOSPHATE 2- / FAD synthase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHuerta, C. / Zhang, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and mechanism of a eukaryotic FMN adenylyltransferase.
Authors: Huerta, C. / Borek, D. / Machius, M. / Grishin, N.V. / Zhang, H.
History
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: FMN Adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7284
Polymers35,9861
Non-polymers7423
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.793, 79.793, 77.941
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein FMN Adenylyltransferase


Mass: 35985.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Strain: NCYC / Gene: CAGL0K01397g, FAD1 / Plasmid: pHIS parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FNA9, FAD synthase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M Sodium acetate, pH 4.4, 6% (w/v) PEG 4000, Temperature 289K, vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 24161 / Num. obs: 24161 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.078 / Χ2: 1.133 / Net I/σ(I): 21.984
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.456 / Num. unique all: 2377 / Rsym value: 0.549 / Χ2: 0.915 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0037refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FWK

3fwk


Resolution: 1.87→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.08 / SU ML: 0.094 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1232 5.1 %RANDOM
Rwork0.174 ---
all0.17661 24132 --
obs0.177 24132 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.58 Å2 / Biso mean: 20.596 Å2 / Biso min: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 44 303 2744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222506
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9823417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5815291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17824.715123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12915427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2621511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021897
X-RAY DIFFRACTIONr_nbd_refined0.2040.21219
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.230
X-RAY DIFFRACTIONr_mcbond_it0.9981.51520
X-RAY DIFFRACTIONr_mcangle_it1.50122379
X-RAY DIFFRACTIONr_scbond_it2.29431170
X-RAY DIFFRACTIONr_scangle_it3.4064.51037
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 86 -
Rwork0.262 1659 -
all-1745 -
obs-1745 99.66 %

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