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- PDB-3dag: The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from M... -

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Basic information

Entry
Database: PDB / ID: 3dag
TitleThe crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / HELIX BUNDLE / 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 / 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
CARBON MONOXIDE / : / Chem-FEG / 5,10-methenyltetrahydromethanopterin hydrogenase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPilak, O. / Warkentin, E. / Shima, S. / Thauer, R.K. / Ermler, U.
CitationJournal: 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
DepositionMay 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 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_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_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.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.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.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_ref_seq_dif.details / _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)39,3635
Polymers38,7091
Non-polymers6544
Water3,675204
1
A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules

A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,72710
Polymers77,4182
Non-polymers1,3098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area7170 Å2
ΔGint-72 kcal/mol
Surface area26720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.930, 95.930, 165.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#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: 38709.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSMZ2661 / Gene: hmd, MJ0784 / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3)(PLYSS)
References: UniProt: Q58194, 5,10-methenyltetrahydromethanopterin hydrogenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-FEG / 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine


Mass: 542.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N6O11P
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50% MPD, 0.1M TRIS/HCL, 20mM NH4H2PO4, 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: 0.99198 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2007 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99198 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 35596 / Num. obs: 35596 / % possible obs: 0.904 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.067 / Rsym value: 0.055 / Net I/σ(I): 16.92
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BOJ

2boj


Resolution: 1.75→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.32 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21994 1886 5 %RANDOM
Rwork0.17943 ---
obs0.1815 35596 95.93 %-
all-35571 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.601 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 42 204 2837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222745
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7272.0073729
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2465343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37425.743101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7515492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.314157
X-RAY DIFFRACTIONr_chiral_restr0.20.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021994
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21350
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21907
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0381.51787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.522818
X-RAY DIFFRACTIONr_scbond_it2.62231097
X-RAY DIFFRACTIONr_scangle_it4.0684.5911
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 133 -
Rwork0.251 2095 -
obs--80.49 %
Refinement TLS params.Method: refined / Origin x: 21.0611 Å / Origin y: 4.9788 Å / Origin z: 19.4654 Å
111213212223313233
T-0.0964 Å2-0.0059 Å2-0.0132 Å2--0.1218 Å2-0.0386 Å2---0.091 Å2
L0.6162 °2-0.1436 °20.3524 °2-0.6422 °2-0.4644 °2--1.6983 °2
S0.0131 Å °0.0055 Å °-0.014 Å °0.0153 Å °0.0336 Å °-0.0371 Å °0.1327 Å °0.055 Å °-0.0467 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3441 - 344
2X-RAY DIFFRACTION1AC501
3X-RAY DIFFRACTION1AF812 - 912

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