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- PDB-3g6k: Crystal Structure of Candida glabrata FMN Adenylyltransferase in ... -

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Basic information

Entry
Database: PDB / ID: 3g6k
TitleCrystal Structure of Candida glabrata FMN Adenylyltransferase in complex with FAD and Inorganic Pyrophosphate
ComponentsFMN adenylyltransferase
KeywordsTRANSFERASE / FAD binding / FAD biosynthesis / alpha/beta protein / Rossmann-like fold / 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 family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / FLAVIN-ADENINE DINUCLEOTIDE / PYROPHOSPHATE 2- / FAD synthase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHuerta, C. / Machius, M. / 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 6, 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 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: FMN adenylyltransferase
B: FMN adenylyltransferase
C: FMN adenylyltransferase
D: FMN adenylyltransferase
E: FMN adenylyltransferase
F: FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,56436
Polymers215,9146
Non-polymers6,64930
Water33,6881870
1
A: FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0206
Polymers35,9861
Non-polymers1,0345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2968
Polymers35,9861
Non-polymers1,3117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9724
Polymers35,9861
Non-polymers9863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1646
Polymers35,9861
Non-polymers1,1785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9724
Polymers35,9861
Non-polymers9863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1418
Polymers35,9861
Non-polymers1,1557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)206.583, 81.481, 136.603
Angle α, β, γ (deg.)90.000, 129.790, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1194-

HOH

21D-755-

HOH

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Components

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Protein / Sugars , 2 types, 7 molecules ABCDEF

#1: Protein
FMN adenylyltransferase


Mass: 35985.723 Da / Num. of mol.: 6
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
#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1899 molecules

#2: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1870 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 22% (w/v) PEG MME 2000, 0.2 M Magnesium sulfate, 0.1 M Sodium acetate, pH 4.8, Temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97874 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 380943 / Num. obs: 380943 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.077 / Χ2: 1.295 / Net I/σ(I): 35.939
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.37 / Num. unique all: 37824 / Rsym value: 0.551 / Χ2: 0.731 / % possible all: 99.8

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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: 1.35→32.19 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.479 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 19043 5 %RANDOM
Rwork0.153 ---
all0.15491 380480 --
obs0.155 380480 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.36 Å2 / Biso mean: 18.537 Å2 / Biso min: 6.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.17 Å2
2---0.07 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.35→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14968 0 417 1870 17255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215808
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.99121586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57751793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92724.498787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.298152711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8991579
X-RAY DIFFRACTIONr_chiral_restr0.0970.22333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211907
X-RAY DIFFRACTIONr_nbd_refined0.2140.37606
X-RAY DIFFRACTIONr_nbtor_refined0.3250.511029
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.52868
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.3259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.5201
X-RAY DIFFRACTIONr_mcbond_it2.01929236
X-RAY DIFFRACTIONr_mcangle_it2.811314778
X-RAY DIFFRACTIONr_scbond_it2.14127948
X-RAY DIFFRACTIONr_scangle_it2.88536801
X-RAY DIFFRACTIONr_rigid_bond_restr1.509312293
X-RAY DIFFRACTIONr_sphericity_free5.062384
X-RAY DIFFRACTIONr_sphericity_bonded4.737311025
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 1367 -
Rwork0.209 26619 -
all-27986 -
obs-27986 99.72 %

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