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- PDB-4jjf: Crystal structure of FE-hydrogenase from methanothermobacter marb... -

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Basic information

Entry
Database: PDB / ID: 4jjf
TitleCrystal structure of FE-hydrogenase from methanothermobacter marburgensis in complex with 2-naphthylisocyanide
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / alpha-beta fold / hydrogenase
Function / homology
Function and homology information


5,10-methenyltetrahydromethanopterin hydrogenase / N5,N10-methenyltetrahydromethanopterin hydrogenase activity / methanogenesis, from carbon dioxide / one-carbon metabolic process
Similarity search - Function
5,10-methenyltetrahydromethanopterin hydrogenase / Hmd, C-terminal helical subdomain / Methenyltetrahydromethanopterin dehydrogenase, Hmd-type / H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal / HMD, C-terminal domain superfamily / H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...5,10-methenyltetrahydromethanopterin hydrogenase / Hmd, C-terminal helical subdomain / Methenyltetrahydromethanopterin dehydrogenase, Hmd-type / H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal / HMD, C-terminal domain superfamily / H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
iron-guanylyl pyridinol cofactor / N-(naphthalen-2-yl)methanimine / 5,10-methenyltetrahydromethanopterin hydrogenase
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTamura, H. / Warkentin, E. / Ermler, U. / Shima, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Crystal structures of [fe]-hydrogenase in complex with inhibitory isocyanides: implications for the h2 -activation site.
Authors: Tamura, H. / Salomone-Stagni, M. / Fujishiro, T. / Warkentin, E. / Meyer-Klaucke, W. / Ermler, U. / Shima, S.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Sep 20, 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_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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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: 5,10-methenyltetrahydromethanopterin hydrogenase
B: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0696
Polymers75,3862
Non-polymers1,6834
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-105 kcal/mol
Surface area26430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.180, 141.180, 96.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 5,10-methenyltetrahydromethanopterin hydrogenase / / H(2)-dependent methylene-H(4)MPT dehydrogenase / H(2)-forming N(5) / N(10)- ...H(2)-dependent methylene-H(4)MPT dehydrogenase / H(2)-forming N(5) / N(10)-methylenetetrahydromethanopterin dehydrogenase / N(5) / N(10)-methenyltetrahydromethanopterin hydrogenase


Mass: 37692.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg
References: UniProt: P32440, 5,10-methenyltetrahydromethanopterin hydrogenase
#2: Chemical ChemComp-FE9 / iron-guanylyl pyridinol cofactor


Mass: 686.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23FeN6O13PS
#3: Chemical ChemComp-N2I / N-(naphthalen-2-yl)methanimine


Mass: 155.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.5mM toluenesulfonylmethylisocyanide, 0.1 M Tris, 0.02 M MgCl2, 30%(v/v) pentaerythritol propoxylate 426, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 41275 / Num. obs: 41275 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.87 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.69
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.77 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.82 / Num. unique all: 5401 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0095refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F46

3f46


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.669 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1808 5 %RANDOM
Rwork0.1708 ---
all0.17347 34050 --
obs0.17347 34050 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.839 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å20 Å2
2--0.35 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 106 152 5534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0261.9777448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1680.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023992
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 132 -
Rwork0.286 2514 -
obs--98.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9143-0.0952-1.1421.7758-0.38874.1689-0.0912-0.3551-0.0670.35520.1402-0.02830.10740.0229-0.0490.15240.04080.01190.06550.02790.175-10.151-23.063-18.356
21.92820.1580.25262.80491.33645.50570.16580.48660.1135-0.4735-0.16970.0631-0.3226-0.64580.00390.23060.1091-0.0250.36680.03720.1754-25.136-0.058-78.123
32.6894-0.96190.78853.3835-1.44242.8119-0.0530.0653-0.1131-0.12030.08810.12680.1216-0.2819-0.03510.0458-0.06660.01420.1089-0.03330.1269-19.675-12.716-48.195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 244
2X-RAY DIFFRACTION1A401 - 405
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B401 - 405
5X-RAY DIFFRACTION3A245 - 344
6X-RAY DIFFRACTION3B245 - 344

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