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- PDB-5a4j: Crystal structure of FTHFS1 from T.acetoxydans Re1 -

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Basic information

Entry
Database: PDB / ID: 5a4j
TitleCrystal structure of FTHFS1 from T.acetoxydans Re1
ComponentsFORMATE--TETRAHYDROFOLATE LIGASE
KeywordsLIGASE / PROTEIN
Function / homology
Function and homology information


formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / tetrahydrofolate interconversion / ATP binding
Similarity search - Function
Formyltetrahydrofolate synthetase; domain 3 / Formyltetrahydrofolate synthetase, domain 3 / Domain 2, N(10)-formyltetrahydrofolate synthetase / Domain 2, N(10)-formyltetrahydrofolate synthetase / Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / P-loop containing nucleotide triphosphate hydrolases ...Formyltetrahydrofolate synthetase; domain 3 / Formyltetrahydrofolate synthetase, domain 3 / Domain 2, N(10)-formyltetrahydrofolate synthetase / Domain 2, N(10)-formyltetrahydrofolate synthetase / Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / DI(HYDROXYETHYL)ETHER / D(-)-TARTARIC ACID / Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesTEPIDANAEROBACTER ACETATOXYDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBergdahl, R. / Jacobson, F. / Muller, B. / Mikkelsen, N. / Schurer, A. / Sandgren, M.
CitationJournal: To be Published
Title: Characterization, Crystallization and Three- Dimensional Structures of Formyltetrahydrofolate Synthetase (Fthfs) from the Syntrophic Acetate Oxidising Bacterium Tepidanaerobacter Acetatoxydans Re1
Authors: Bergdahl, R. / Jacobson, F. / Muller, B. / Mikkelsen, N. / Schurer, A. / Sandgren, M.
History
DepositionJun 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: FORMATE--TETRAHYDROFOLATE LIGASE
B: FORMATE--TETRAHYDROFOLATE LIGASE
C: FORMATE--TETRAHYDROFOLATE LIGASE
D: FORMATE--TETRAHYDROFOLATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,87028
Polymers242,0944
Non-polymers1,77524
Water17,132951
1
C: FORMATE--TETRAHYDROFOLATE LIGASE
D: FORMATE--TETRAHYDROFOLATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5389
Polymers121,0472
Non-polymers4917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-22.8 kcal/mol
Surface area38720 Å2
MethodPISA
2
A: FORMATE--TETRAHYDROFOLATE LIGASE
B: FORMATE--TETRAHYDROFOLATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,33219
Polymers121,0472
Non-polymers1,28417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-3.6 kcal/mol
Surface area38880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.038, 100.980, 258.050
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, 4 molecules ABCD

#1: Protein
FORMATE--TETRAHYDROFOLATE LIGASE / FORMYLTETRAHYDROFOLATE SYNTHETASE / FORMYLTETRAHYDROFOLATE SYNTHETASE


Mass: 60523.598 Da / Num. of mol.: 4 / Fragment: ENZYMATIC DOMAIN, UNP RESIDUES 1-559
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TEPIDANAEROBACTER ACETATOXYDANS (bacteria)
Strain: RE1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: K7SWE7, formate-tetrahydrofolate ligase

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Non-polymers , 7 types, 975 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 951 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAMINO ACID RESIDUE 372 HAS ACCIDENTALY BEEN MUTATED TO A THREONIN IN THE PROTEIN. NORMALLY IT IS AN ...AMINO ACID RESIDUE 372 HAS ACCIDENTALY BEEN MUTATED TO A THREONIN IN THE PROTEIN. NORMALLY IT IS AN ALANIN RESIDUE.

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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: 2.34 Å3/Da / Density % sol: 47.49 % / Description: NONE
Crystal growpH: 6.5
Details: 0.20 M SODIUM-POTASSIUM TARTRATE 0.10 M BIS-TRIS PROPANE PH 6.5 18% W/V POLYETHYLENE GLYCOL (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 1.04088
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04088 Å / Relative weight: 1
ReflectionResolution: 2.15→29.6 Å / Num. obs: 126940 / % possible obs: 98.9 % / Observed criterion σ(I): 3.8 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.7 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RBO

3rbo
PDB Unreleased entry


Resolution: 2.15→29.62 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.854 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22021 6351 5 %RANDOM
Rwork0.18397 ---
obs0.18579 120401 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16906 0 104 951 17961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01917381
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217308
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.98423487
X-RAY DIFFRACTIONr_angle_other_deg0.692339893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.20652257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8925.222722
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.792153112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5221588
X-RAY DIFFRACTIONr_chiral_restr0.0550.22697
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02119711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023605
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 458 -
Rwork0.254 8727 -
obs--98.29 %

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