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- PDB-2phn: Crystal structure of an amide bond forming F420-gamma glutamyl li... -

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Basic information

Entry
Database: PDB / ID: 2phn
TitleCrystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus
ComponentsF420-0:gamma-glutamyl ligase
KeywordsLIGASE / gamma-glutamyl ligase / coenzyme F420 biosynthesis / amide bond forming enzyme / metal dependent / new fold / GDP binding / MCSG / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase / coenzyme F420-0:L-glutamate ligase activity / coenzyme F420-1:gamma-L-glutamate ligase activity / F420-0 metabolic process / GTP binding / metal ion binding
Similarity search - Function
CofE-like / CofE-like fold / CofE-like domain / Coenzyme F420:L-glutamate ligase, archaeal / Coenzyme F420:L-glutamate ligase-like domain / Coenzyme F420:L-glutamate ligase / F420-0:Gamma-glutamyl ligase / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-DIPHOSPHATE / : / Coenzyme F420:L-glutamate ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsNocek, B. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of an Amide Bond Forming F(420):gammagamma-glutamyl Ligase from Archaeoglobus Fulgidus - A Member of a New Family of Non-ribosomal Peptide Synthases.
Authors: Nocek, B. / Evdokimova, E. / Proudfoot, M. / Kudritska, M. / Grochowski, L.L. / White, R.H. / Savchenko, A. / Yakunin, A.F. / Edwards, A. / Joachimiak, A.
History
DepositionApr 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 19, 2011Group: Derived calculations
Revision 1.4Aug 30, 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_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.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.pdbx_leaving_atom_flag / _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
Revision 1.5Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT ASSEMBLY HAS BEEN CONFIRMED BY GEL FILTRATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F420-0:gamma-glutamyl ligase
B: F420-0:gamma-glutamyl ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,20817
Polymers55,5262
Non-polymers1,68315
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-75 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.367, 98.367, 94.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein F420-0:gamma-glutamyl ligase


Mass: 27762.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126 / Gene: cofE, AF_2256 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold
References: UniProt: O28028, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 6 types, 591 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate, 25% PEG 5000 MME, 10 mM GDP, MnCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2006 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. all: 99727 / Num. obs: 99727 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.3
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.69 / Num. unique all: 4897 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G9I

2g9i


Resolution: 1.35→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.678 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18997 4973 5 %RANDOM
Rwork0.1603 ---
all0.164 99727 --
obs0.16179 94754 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 98 576 4483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224258
X-RAY DIFFRACTIONr_bond_other_d0.0020.022987
X-RAY DIFFRACTIONr_angle_refined_deg1.5642.0195804
X-RAY DIFFRACTIONr_angle_other_deg0.9553.0027300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18723.73185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47215780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5151545
X-RAY DIFFRACTIONr_chiral_restr0.0920.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024849
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02858
X-RAY DIFFRACTIONr_nbd_refined0.2260.2860
X-RAY DIFFRACTIONr_nbd_other0.2060.23390
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22120
X-RAY DIFFRACTIONr_nbtor_other0.0860.22388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2398
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4931.52863
X-RAY DIFFRACTIONr_mcbond_other0.5811.51089
X-RAY DIFFRACTIONr_mcangle_it2.00924319
X-RAY DIFFRACTIONr_scbond_it2.62931706
X-RAY DIFFRACTIONr_scangle_it3.7034.51466
X-RAY DIFFRACTIONr_rigid_bond_restr2.30637965
X-RAY DIFFRACTIONr_sphericity_free5.9613590
X-RAY DIFFRACTIONr_sphericity_bonded3.23837162
LS refinement shellResolution: 1.35→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 363 -
Rwork0.164 6863 -
obs--97.97 %

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