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- PDB-6k8c: Crystal structure of Helicobacter pylori folylpolyglutamate synthetase -

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Basic information

Entry
Database: PDB / ID: 6k8c
TitleCrystal structure of Helicobacter pylori folylpolyglutamate synthetase
ComponentsFolylpolyglutamate synthase (FolC)
KeywordsLIGASE / Folylpolyglutamate synthetase / Dihydropteroate synthetase / FolC / Bifunctional FolC
Function / homology
Function and homology information


tetrahydrofolate synthase / dihydrofolate synthase activity / folic acid-containing compound biosynthetic process / tetrahydrofolylpolyglutamate synthase activity / tetrahydrofolate biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Folylpolyglutamate synthetase / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
CITRIC ACID / tetrahydrofolate synthase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95174964908 Å
AuthorsPark, J.S. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2013M3A6A4043695 Korea, Republic Of
CitationJournal: Crystals / Year: 2019
Title: Structural Analyses of Helicobacter Pylori FolC Conducting Glutamation in Folate Metabolism.
Authors: Park, J.S. / Kim, H.S. / Park, S.H. / Park, M.S. / Kang, S.-M. / Kim, H.-J. / Han, B.W.
History
DepositionJun 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Folylpolyglutamate synthase (FolC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2973
Polymers46,0131
Non-polymers2842
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint1 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.454, 61.637, 69.743
Angle α, β, γ (deg.)90.000, 115.962, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Folylpolyglutamate synthase (FolC)


Mass: 46013.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Gene: HP_1545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O26070, tetrahydrofolate synthase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 36178 / % possible obs: 98.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 33.8943026253 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Χ2: 1.048 / Net I/σ(I): 26.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 4.24 / Num. unique obs: 1800 / CC1/2: 0.962 / Rpim(I) all: 0.169 / Rrim(I) all: 0.463 / Χ2: 1.093 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95174964908→29.9363061017 Å / SU ML: 0.189827748035 / Cross valid method: FREE R-VALUE / σ(F): 1.33481014704 / Phase error: 23.5747107896
RfactorNum. reflection% reflection
Rfree0.219420757096 1808 4.99847944486 %
Rwork0.18422746775 --
obs0.185993051755 36171 98.7631061599 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.2176693653 Å2
Refinement stepCycle: LAST / Resolution: 1.95174964908→29.9363061017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 19 314 3362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003632615771913102
X-RAY DIFFRACTIONf_angle_d0.6395756445964179
X-RAY DIFFRACTIONf_chiral_restr0.0440257098043477
X-RAY DIFFRACTIONf_plane_restr0.00376088054472528
X-RAY DIFFRACTIONf_dihedral_angle_d9.740400260751879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95174964908-2.00450.2562645657781360.239183028432258297.3844500179
2.0045-2.06350.2962995993811400.222938992789264899.2170818505
2.0635-2.13010.2463140691131380.218049115815263999.3559928444
2.1301-2.20620.2549619467851410.208894737595266299.432422845
2.2062-2.29450.2514301526361370.198580348744262999.5680345572
2.2945-2.39890.2779985613711400.207748263625266099.7150997151
2.3989-2.52530.2486711953171410.204954534669266199.8218738867
2.5253-2.68340.2314447538731410.200854540699267599.8227578873
2.6834-2.89040.2352655708131400.200249735229266899.9288256228
2.8904-3.1810.2214971301661400.198210918193266399.9643366619
3.181-3.64060.2349591790761420.178720317029268599.682651622
3.6406-4.58410.1662184291261380.154445484406264097.7480647431
4.58410.1951144406191340.164299983973255192.490527041

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