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- PDB-5vyq: Crystal structure of the N-formyltransferase Rv3404c from mycobac... -

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Basic information

Entry
Database: PDB / ID: 5vyq
TitleCrystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid
ComponentsUncharacterized protein
KeywordsTRANSFERASE / formyltransferase / deoxysugar
Function / homology
Function and homology information


hydroxymethyl-, formyl- and related transferase activity / biosynthetic process
Similarity search - Function
N-formyltransferase dimerization C-terminal domain / N-formyltransferase dimerization C-terminal domain / Formyl transferase, N-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
dTDP-4-amino-4,6-dideoxyglucose / Chem-EP1 / Chem-FON / : / : / THYMIDINE-5'-DIPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis CAS/NITR204 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDunsirn, M.M. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Biochemistry / Year: 2017
Title: Biochemical Investigation of Rv3404c from Mycobacterium tuberculosis.
Authors: Dunsirn, M.M. / Thoden, J.B. / Gilbert, M. / Holden, H.M.
History
DepositionMay 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,48820
Polymers58,0672
Non-polymers2,42018
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-77 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.486, 73.018, 173.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 29033.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CAS/NITR204 (bacteria)
Gene: J113_23825 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: R4MIX2

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Non-polymers , 10 types, 684 molecules

#2: Chemical ChemComp-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#3: Chemical ChemComp-0FX / dTDP-4-amino-4,6-dideoxyglucose


Mass: 547.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EP1 / 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID / HEPPS (buffer)


Mass: 252.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20N2O4S / Comment: pH buffer*YM
#8: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#9: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG-8000, 100 mM HEPPS, 200 mM KCl, 5 mM TDP-Qui4N, 5 mM folinic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 20, 2017 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 79772 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.4
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 12792 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pzu

4pzu


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.872 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20025 3990 5 %RANDOM
Rwork0.16673 ---
obs0.16841 75782 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.699 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.64 Å2
Refinement stepCycle: 1 / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 151 666 4558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194003
X-RAY DIFFRACTIONr_bond_other_d0.0010.023763
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9755439
X-RAY DIFFRACTIONr_angle_other_deg0.93838618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21123.237207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65515630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1921539
X-RAY DIFFRACTIONr_chiral_restr0.1120.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7611.4311887
X-RAY DIFFRACTIONr_mcbond_other1.7561.4291886
X-RAY DIFFRACTIONr_mcangle_it2.5742.1312356
X-RAY DIFFRACTIONr_mcangle_other2.5752.1332357
X-RAY DIFFRACTIONr_scbond_it2.9641.8052116
X-RAY DIFFRACTIONr_scbond_other2.9551.8062116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5392.583079
X-RAY DIFFRACTIONr_long_range_B_refined6.56714.025095
X-RAY DIFFRACTIONr_long_range_B_other6.56714.0255096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 298 -
Rwork0.292 5378 -
obs--96.02 %

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