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- PDB-2fhj: Crystal structure of formylmethanofuran: tetrahydromethanopterin ... -

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Basic information

Entry
Database: PDB / ID: 2fhj
TitleCrystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes
Components(Formylmethanofuran--tetrahydromethanopterin ...) x 2
KeywordsTRANSFERASE / tetrahydromethanopterin / methanofuran / C1 metabolism / formyltransferase / complex
Function / homology
Function and homology information


formylmethanofuran-tetrahydromethanopterin N-formyltransferase / formylmethanofuran-tetrahydromethanopterin N-formyltransferase activity / methanogenesis, from carbon dioxide / 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
Chem-H4Z / : / Chem-MFN / Chem-PE3 / Formylmethanofuran--tetrahydromethanopterin formyltransferase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAcharya, P. / Warkentin, E. / Thauer, R.K. / Shima, S. / Ermler, U.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes
Authors: Acharya, P. / Warkentin, E. / Ermler, U. / Thauer, R.K. / Shima, S.
History
DepositionDec 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ncs_dom_lim / 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 / _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.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.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,84131
Polymers126,7624
Non-polymers7,07927
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27880 Å2
ΔGint-99 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.000, 74.150, 103.870
Angle α, β, γ (deg.)90.00, 113.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
12C
22D
32C
42D
52C
62D
72C
82D
92C
102D
112C
122D
132C
142D
152C
162D
172C
182D
192C
202D
212C
222D
232C
242D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASNASN2AA1 - 41 - 4
211METMETASNASN2BB1 - 41 - 4
321GLYGLYPROPRO1AA5 - 635 - 63
421GLYGLYPROPRO1BB5 - 635 - 63
531GLUGLUGLYGLY1AA65 - 12865 - 128
631GLUGLUGLYGLY1BB65 - 12865 - 128
741GLYGLYALAALA1AA130 - 208130 - 208
841GLYGLYALAALA1BB130 - 208130 - 208
951ASNASNPHEPHE1AA234 - 296234 - 296
1051ASNASNPHEPHE1BB234 - 296234 - 296
1161ALAALATHRTHR1AA226 - 230226 - 230
1261ALAALATHRTHR1BB226 - 230226 - 230
112METMETASNASN5CC1 - 41 - 4
212METMETASNASN5DD1 - 41 - 4
322GLYGLYALAALA1CC5 - 335 - 33
422GLYGLYALAALA1DD5 - 335 - 33
532ILEILEILEILE1CC35 - 4835 - 48
632ILEILEILEILE1DD35 - 4835 - 48
742CYSCYSGLUGLU1CC50 - 6450 - 64
842CYSCYSGLUGLU1DD50 - 6450 - 64
952THRTHRMETMET1CC66 - 10966 - 109
1052THRTHRMETMET1DD66 - 10966 - 109
1162LYSLYSGLYGLY1CC114 - 121114 - 121
1262LYSLYSGLYGLY1DD114 - 121114 - 121
1372LYSLYSGLUGLU1CC123 - 136123 - 136
1472LYSLYSGLUGLU1DD123 - 136123 - 136
1582GLYGLYALAALA1CC139 - 208139 - 208
1682GLYGLYALAALA1DD139 - 208139 - 208
1792LEULEUILEILE1CC236 - 264236 - 264
1892LEULEUILEILE1DD236 - 264236 - 264
19102ALAALAGLYGLY1CC266 - 279266 - 279
20102ALAALAGLYGLY1DD266 - 279266 - 279
21112ILEILEPHEPHE2CC290 - 296290 - 296
22112ILEILEPHEPHE2DD290 - 296290 - 296
23122ALAALATHRTHR1CC226 - 230226 - 230
24122ALAALATHRTHR1DD226 - 230226 - 230

NCS ensembles :
ID
1
2

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Components

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Formylmethanofuran--tetrahydromethanopterin ... , 2 types, 4 molecules ABCD

#1: Protein Formylmethanofuran--tetrahydromethanopterin formyltransferase / E.C.2.3.1.101 / H4MPT formyltransferase


Mass: 31686.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: FTR / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q49610, formylmethanofuran-tetrahydromethanopterin N-formyltransferase
#2: Protein Formylmethanofuran--tetrahydromethanopterin formyltransferase / E.C.2.3.1.101 / H4MPT formyltransferase


Mass: 31702.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS D 58 hydroxylated / Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: FTR / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q49610, formylmethanofuran-tetrahydromethanopterin N-formyltransferase

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Non-polymers , 6 types, 478 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MFN / N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE


Mass: 776.741 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H44N4O16
#5: Chemical ChemComp-H4Z / 5-(4-{[1-(2-AMINO-5-FORMYL-7-METHYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL)ETHYL]AMINO}PHENYL)-5-DEOXY-1-O-{5-O-[(1,3-DICARBOXYPROPOXY)(HYDROXY)PHOSPHORYL]PENTOFURANOSYL}PENTITOL


Mass: 804.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H45N6O17P
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12-18 % PEG 8000, 20 % glycerol, 0.5 M KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2004
RadiationMonochromator: Si111 or Si311 crystals, LN2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→104 Å / Num. all: 77164 / Num. obs: 75995 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.126 / Rsym value: 0.105 / Net I/σ(I): 7.93
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.38 / Num. unique all: 9923 / Num. unique obs: 9923 / Rsym value: 0.413 / % possible all: 91.7

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Phasing

Phasing MRRfactor: 0.351 / Cor.coef. Fo:Fc: 0.667
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
XSCALEdata scaling
EPMRphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1FTR

1ftr


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.699 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3870 5 %RANDOM
Rwork0.219 ---
all0.221 75995 --
obs0.221 75995 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.712 Å2
Baniso -1Baniso -2Baniso -3
1-4.91 Å20 Å21.84 Å2
2---2.9 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8950 0 417 451 9818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229551
X-RAY DIFFRACTIONr_bond_other_d0.0060.028170
X-RAY DIFFRACTIONr_angle_refined_deg1.613212901
X-RAY DIFFRACTIONr_angle_other_deg1.77319127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3115.0171211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87626.02407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.148151455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4271524
X-RAY DIFFRACTIONr_chiral_restr0.0720.21355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210776
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021717
X-RAY DIFFRACTIONr_nbd_refined0.2540.22393
X-RAY DIFFRACTIONr_nbd_other0.1930.29060
X-RAY DIFFRACTIONr_nbtor_refined0.1910.24756
X-RAY DIFFRACTIONr_nbtor_other0.0910.25479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.217
X-RAY DIFFRACTIONr_mcbond_it1.1361.55944
X-RAY DIFFRACTIONr_mcbond_other0.3711.52475
X-RAY DIFFRACTIONr_mcangle_it1.85629507
X-RAY DIFFRACTIONr_scbond_it3.4543.53656
X-RAY DIFFRACTIONr_scangle_it5.22353390
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3724TIGHT POSITIONAL0.050.05
1A28MEDIUM POSITIONAL0.060.5
1A3724TIGHT THERMAL0.080.5
1A28MEDIUM THERMAL0.192
2C3279TIGHT POSITIONAL0.040.05
2C97MEDIUM POSITIONAL0.060.5
2C33LOOSE POSITIONAL0.085
2C3279TIGHT THERMAL0.10.5
2C97MEDIUM THERMAL0.322
2C33LOOSE THERMAL1.0910
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 289 -
Rwork0.34 5228 -
obs-5517 94.57 %

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