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- PDB-6nbp: Crystal Structure of a Sugar N-Formyltransferase from the Plant P... -

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Basic information

Entry
Database: PDB / ID: 6nbp
TitleCrystal Structure of a Sugar N-Formyltransferase from the Plant Pathogen Pantoea ananatis
ComponentsN-formyltransferase
KeywordsTRANSFERASE / sugar biosynthesis / o-antigen / pantoea
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 / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / 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-FON / PHOSPHATE ION / N-formyltransferase
Similarity search - Component
Biological speciesPantoea ananatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHofmeister, D.L. / 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: Protein Sci. / Year: 2019
Title: Investigation of a sugar N-formyltransferase from the plant pathogen Pantoea ananatis.
Authors: Hofmeister, D.L. / Thoden, J.B. / Holden, H.M.
History
DepositionDec 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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_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.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.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1905
Polymers30,0511
Non-polymers1,1394
Water4,522251
1
A: N-formyltransferase
hetero molecules

A: N-formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,38010
Polymers60,1022
Non-polymers2,2778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area4330 Å2
ΔGint-50 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.928, 75.928, 87.591
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21A-593-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-formyltransferase


Mass: 30051.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pantoea ananatis (bacteria) / Strain: NFR11 / Gene: SAMN03097714_1080 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: A0A4P1LYI6*PLUS

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Non-polymers , 5 types, 255 molecules

#2: Chemical ChemComp-0FX / dTDP-4-amino-4,6-dideoxyglucose


Mass: 547.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N3O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 13-16%PEG-3350, 2 mM folinic acid, 5 mM dTDP-Qui4N, 200 mM NaCl, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 32264 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4954 / Rsym value: 0.433 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFV

4yfv


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.943 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22646 1537 4.8 %RANDOM
Rwork0.18574 ---
obs0.18764 30727 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----1.56 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 56 251 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0152095
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171846
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.772848
X-RAY DIFFRACTIONr_angle_other_deg0.5041.724330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7865252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09120.34587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25115311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7981513
X-RAY DIFFRACTIONr_chiral_restr0.0680.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
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_it2.2482.517990
X-RAY DIFFRACTIONr_mcbond_other2.2472.518991
X-RAY DIFFRACTIONr_mcangle_it3.393.7531236
X-RAY DIFFRACTIONr_mcangle_other3.3883.7541237
X-RAY DIFFRACTIONr_scbond_it2.8752.8341105
X-RAY DIFFRACTIONr_scbond_other2.822.8191102
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3954.1131602
X-RAY DIFFRACTIONr_long_range_B_refined6.40731.362370
X-RAY DIFFRACTIONr_long_range_B_other6.31230.6862296
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 107 -
Rwork0.351 2096 -
obs--91.79 %

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