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- PDB-1m5h: Formylmethanofuran:tetrahydromethanopterin formyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 1m5h
TitleFormylmethanofuran:tetrahydromethanopterin formyltransferase from Archaeoglobus fulgidus
ComponentsFormylmethanofuran--tetrahydromethanopterin formyltransferase
KeywordsTRANSFERASE / ALPHA/BETA SANDWICH
Function / homology
Function and homology information


formylmethanofuran-tetrahydromethanopterin N-formyltransferase / formylmethanofuran-tetrahydromethanopterin N-formyltransferase activity / lactate oxidation / one-carbon metabolic process / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #520 / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, C-terminal / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, N-terminal / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, ferredoxin-like superfamily / Formylmethanofuran-tetrahydromethanopterin formyltransferase / FTR, proximal lobe / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Formylmethanofuran--tetrahydromethanopterin formyltransferase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMamat, B. / Roth, A. / Grimm, C. / Ermler, U. / Tziatzios, C. / Schubert, D. / Thauer, R.K. / Shima, S.
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship.
Authors: Mamat, B. / Roth, A. / Grimm, C. / Ermler, U. / Tziatzios, C. / Schubert, D. / Thauer, R.K. / Shima, S.
History
DepositionJul 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formylmethanofuran--tetrahydromethanopterin formyltransferase
B: Formylmethanofuran--tetrahydromethanopterin formyltransferase
C: Formylmethanofuran--tetrahydromethanopterin formyltransferase
D: Formylmethanofuran--tetrahydromethanopterin formyltransferase
E: Formylmethanofuran--tetrahydromethanopterin formyltransferase
F: Formylmethanofuran--tetrahydromethanopterin formyltransferase
G: Formylmethanofuran--tetrahydromethanopterin formyltransferase
H: Formylmethanofuran--tetrahydromethanopterin formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,55632
Polymers253,6188
Non-polymers93824
Water32,3191794
1
A: Formylmethanofuran--tetrahydromethanopterin formyltransferase
B: Formylmethanofuran--tetrahydromethanopterin formyltransferase
C: Formylmethanofuran--tetrahydromethanopterin formyltransferase
D: Formylmethanofuran--tetrahydromethanopterin formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,27816
Polymers126,8094
Non-polymers46912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19710 Å2
ΔGint-117 kcal/mol
Surface area39460 Å2
MethodPISA
2
E: Formylmethanofuran--tetrahydromethanopterin formyltransferase
F: Formylmethanofuran--tetrahydromethanopterin formyltransferase
G: Formylmethanofuran--tetrahydromethanopterin formyltransferase
H: Formylmethanofuran--tetrahydromethanopterin formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,27816
Polymers126,8094
Non-polymers46912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19530 Å2
ΔGint-119 kcal/mol
Surface area39560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 81.810, 99.100
Angle α, β, γ (deg.)90.10, 110.04, 93.75
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
Formylmethanofuran--tetrahydromethanopterin formyltransferase / E.C.2.3.1.101 / Formylmethanofuran:Tetrahydromethanopterin formyltransferase / ftr-2 / ftr-2 AF2207


Mass: 31702.188 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET24b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O28076, formylmethanofuran-tetrahydromethanopterin N-formyltransferase
#2: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1794 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Imidazol/Malate, KSCN, PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
210 mMMOPS1droppH7.0
30.1 Mimidazole-malate1reservoir
40.2 MKSCN1reservoir
523 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8452 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8452 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 175340 / Num. obs: 150792 / % possible obs: 86 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 5.2 Å2 / Rsym value: 0.08
Reflection shellResolution: 2→2.1 Å / Rsym value: 0.223 / % possible all: 67
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 86 % / Num. measured all: 839340 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 67 % / Rmerge(I) obs: 0.223

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Formylmethanofuran:Tetrahydromethanopterin Formyltransferase from Methanosarcina barkeri

Resolution: 2→29.25 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.282 6405 5.1 %RANDOM
Rwork0.229 ---
all0.229 175340 --
obs0.229 150792 82.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.8486 Å2 / ksol: 0.346027 e/Å3
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20.51 Å22.24 Å2
2---0.21 Å20.6 Å2
3----2.43 Å2
Refine analyzeLuzzati coordinate error free: 0.33 Å / Luzzati sigma a free: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17840 0 24 1794 19658
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it3.032
X-RAY DIFFRACTIONc_scangle_it3.862.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 841 5.3 %
Rwork0.248 15090 -
obs-15931 62.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.229 / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.31 / Rfactor Rwork: 0.248

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