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- PDB-3g5a: Crystal Structure of Candida glabrata FMN Adenylyltransferase in ... -

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Basic information

Entry
Database: PDB / ID: 3g5a
TitleCrystal Structure of Candida glabrata FMN Adenylyltransferase in complex with FMN and ATP analog AMPCPP
ComponentsFMN adenylyltransferase
KeywordsTRANSFERASE / FMN binding / ATP 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / FLAVIN MONONUCLEOTIDE / FAD synthase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _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
B: FMN adenylyltransferase
C: FMN adenylyltransferase
D: FMN adenylyltransferase
E: FMN adenylyltransferase
F: FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,92625
Polymers215,9146
Non-polymers6,01119
Water32,2471790
1
A: 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
2
B: 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
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)37,0685
Polymers35,9861
Non-polymers1,0824
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)36,9724
Polymers35,9861
Non-polymers9863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)207.831, 81.753, 136.698
Angle α, β, γ (deg.)90.000, 129.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-351-

HOH

21D-1226-

HOH

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Components

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Protein , 1 types, 6 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

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Non-polymers , 5 types, 1809 molecules

#2: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1790 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium acetate, pH 4.6, 8% (w/v) PEG 4000, temperature 293K, 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: Nov 13, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 123738 / Num. obs: 123738 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.088 / Χ2: 1.112 / Net I/σ(I): 11.517
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.094 / Num. unique all: 12367 / Rsym value: 0.447 / Χ2: 0.999 / % possible all: 97.1

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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: 1.95→35.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.18 / SU B: 4.038 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 6202 5 %RANDOM
Rwork0.175 ---
all0.17845 123713 --
obs0.178 123713 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.94 Å2 / Biso mean: 19.286 Å2 / Biso min: 4.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.32 Å2
2---0.16 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14700 0 397 1790 16887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215515
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.99121184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10551778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46624.628752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.282152604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0151568
X-RAY DIFFRACTIONr_chiral_restr0.0940.22285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211678
X-RAY DIFFRACTIONr_nbd_refined0.20.27449
X-RAY DIFFRACTIONr_nbtor_refined0.3050.210629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.21502
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.2243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.283
X-RAY DIFFRACTIONr_mcbond_it1.27429256
X-RAY DIFFRACTIONr_mcangle_it1.963314542
X-RAY DIFFRACTIONr_scbond_it1.2427588
X-RAY DIFFRACTIONr_scangle_it1.83536636
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 432 -
Rwork0.225 8606 -
all-9038 -
obs-9038 95.54 %

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