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- PDB-1fpm: MONOVALENT CATION BINDING SITES IN N10-FORMYLTETRAHYDROFOLATE SYN... -

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Basic information

Entry
Database: PDB / ID: 1fpm
TitleMONOVALENT CATION BINDING SITES IN N10-FORMYLTETRAHYDROFOLATE SYNTHETASE FROM MOORELLA THERMOACETICA
ComponentsFORMATE--TETRAHYDROFOLATE LIGASE
KeywordsLIGASE / MONOVALENT CATION / THERMOSTABLE / TETRAMER
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
: / Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsRadfar, R. / Leaphart, A. / Brewer, J.M. / Minor, W. / Odom, J.D.
CitationJournal: Biochemistry / Year: 2000
Title: Cation binding and thermostability of FTHFS monovalent cation binding sites and thermostability of N10-formyltetrahydrofolate synthetase from Moorella thermoacetica.
Authors: Radfar, R. / Leaphart, A. / Brewer, J.M. / Minor, W. / Odom, J.D. / Dunlap, R.B. / Lovell, C.R. / Lebioda, L.
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,99415
Polymers119,6722
Non-polymers1,32313
Water4,864270
1
A: FORMATE--TETRAHYDROFOLATE LIGASE
B: FORMATE--TETRAHYDROFOLATE LIGASE
hetero molecules

A: FORMATE--TETRAHYDROFOLATE LIGASE
B: FORMATE--TETRAHYDROFOLATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,98830
Polymers239,3434
Non-polymers2,64526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
2
A: FORMATE--TETRAHYDROFOLATE LIGASE
hetero molecules

B: FORMATE--TETRAHYDROFOLATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,99415
Polymers119,6722
Non-polymers1,32313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8110 Å2
ΔGint-257 kcal/mol
Surface area38900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.876, 160.876, 256.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 59835.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Plasmid: PCRL47 S2A / Production host: Escherichia coli (E. coli)
References: UniProt: P21164, formate-tetrahydrofolate ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: AMMONIUM SULFATE, PEG 1000, POTASSIUM MALEATE, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
146 %satammonium sulfate1reservoir
21 mMdithiothreitol1reservoir
31 %PEG10001reservoir
450 mMpotassium maleate1reservoirpH7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 137437 / Num. obs: 25025 / % possible obs: 97 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.99→3.1 Å / Rmerge(I) obs: 0.182 / % possible all: 94.7
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 97 % / Num. measured all: 137437

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 3→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 387313.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.32 3922 9.5 %RANDOM
Rwork0.266 ---
obs0.266 41458 84 %-
all-137437 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.28 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å25.94 Å20 Å2
2--2.66 Å20 Å2
3----5.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8258 0 57 270 8585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 540 9.7 %
Rwork0.302 5025 -
obs--67.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 3 / % reflection Rfree: 9.5 % / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.359 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.302

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