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- PDB-3f47: The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from M... -

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Basic information

Entry
Database: PDB / ID: 3f47
TitleThe Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / HELIX BUNDLE / COMPLEX WITH IRON GUANYLYL PYRIDINOL COFACTOR / Methanogenesis / One-carbon metabolism
Function / homology
Function and homology information


5,10-methenyltetrahydromethanopterin hydrogenase / N5,N10-methenyltetrahydromethanopterin hydrogenase activity / methanogenesis, from carbon dioxide / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / 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 / HMD N-terminal domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) ...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 / HMD N-terminal domain / 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
CARBON MONOXIDE / : / Chem-I2C / 5,10-methenyltetrahydromethanopterin hydrogenase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsHiromoto, T. / Pilak, O. / Warkentin, E. / Thauer, R.K. / Shima, S. / Ermler, U.
Citation
Journal: Febs Lett. / Year: 2009
Title: The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex.
Authors: Hiromoto, T. / Ataka, K. / Pilak, O. / Vogt, S. / Stagni, M.S. / Meyer-Klaucke, W. / Warkentin, E. / Thauer, R.K. / Shima, S. / Ermler, U.
#1: Journal: Science / Year: 2008
Title: The Crystal Structure of [Fe]-Hydrogenase Reveals the Geometry of the Active Site
Authors: Shima, S. / Pilak, O. / Vogt, S. / Schick, M. / Stagni, M.S. / Meyer-Klaucke, W. / Warkentin, E. / Thauer, R.K. / Ermler, U.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4006
Polymers38,7391
Non-polymers6615
Water4,288238
1
A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules

A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,80112
Polymers77,4782
Non-polymers1,32210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area8480 Å2
ΔGint-127 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.930, 95.930, 165.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 38739.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: hmd, MJ0784 / Plasmid: pET-24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q58194, 5,10-methenyltetrahydromethanopterin hydrogenase

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Non-polymers , 5 types, 243 molecules

#2: Chemical ChemComp-I2C / 5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine


Mass: 526.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N6O10P
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50% MPD, 100mM Tris-HCl, 20mM Ammonium dihydrogen phosphate, 1mM DTT , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.992 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2007 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 1.75→26.2 Å / Num. obs: 37583 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 32.677 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 9296 / Num. unique all: 9296 / Num. unique obs: 2563 / % possible all: 81.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
XDSdata reduction
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3DAG

3dag


Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.862 / SU B: 4.613 / SU ML: 0.074 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1887 5 %RANDOM
Rwork0.173 ---
obs0.174 37574 95.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.58 Å2 / Biso mean: 33.553 Å2 / Biso min: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.65 Å2
Refine analyzeLuzzati coordinate error obs: 0.243 Å
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 42 238 2873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222818
X-RAY DIFFRACTIONr_angle_refined_deg1.5782.0073853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71325.784102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39715493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.905157
X-RAY DIFFRACTIONr_chiral_restr0.110.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022110
X-RAY DIFFRACTIONr_nbd_refined0.2030.21381
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.219
X-RAY DIFFRACTIONr_mcbond_it0.7491.51802
X-RAY DIFFRACTIONr_mcangle_it1.29422933
X-RAY DIFFRACTIONr_scbond_it2.47431047
X-RAY DIFFRACTIONr_scangle_it3.9784.5920
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 98 -
Rwork0.255 2205 -
all-2303 -
obs-2303 81.12 %
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)
13.26110.2209-0.14661.41310.02661.97710.0277-0.219-0.14250.18160.02320.00950.27770.037-0.0509-0.06410.0104-0.0431-0.16250.0043-0.1520.6872-1.604333.0099
22.52410.83590.25622.1824-0.22062.1095-0.0110.1280.082-0.06870.0133-0.23750.06720.3241-0.0024-0.15330.0302-0.0276-0.1026-0.0195-0.116832.61336.257820.5073
32.7778-0.10811.37622.001-0.16034.6790.08360.255-0.0414-0.2346-0.0172-0.03010.11420.1588-0.0664-0.1176-0.01660.002-0.1351-0.006-0.144319.08458.5403-2.5684
42.66790.39911.02044.46970.81684.35310.015-0.0122-0.0097-0.00630.12390.22450.0132-0.3498-0.1389-0.1356-0.0318-0.0075-0.08120.0483-0.16585.201417.732-3.6195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 154
2X-RAY DIFFRACTION2A155 - 240
3X-RAY DIFFRACTION3A241 - 286
4X-RAY DIFFRACTION4A287 - 345

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