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- PDB-3f46: The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Hol... -

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Entry
Database: PDB / ID: 3f46
TitleThe Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / HELIX BUNDLE / COMPLEX WITH IRON GUANYLYL PYRIDINOL COFACTOR / C176A MUTANT / 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 / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / : / Chem-I2C / 5,10-methenyltetrahydromethanopterin hydrogenase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsHiromoto, T. / Vogt, S. / Warkentin, E. / Thauer, R.K. / Shima, S. / Ermler, U.
CitationJournal: 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.
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 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _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 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5006
Polymers38,7071
Non-polymers7935
Water3,045169
1
A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules

A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,99912
Polymers77,4142
Non-polymers1,58510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area8990 Å2
ΔGint-120 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.350, 96.350, 166.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

21A-520-

HOH

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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: 38707.004 Da / Num. of mol.: 1 / Mutation: C176A
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, 174 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-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 49% MPD, 100mM Tris-HCl, 50mM 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: 0.9919 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2008 / 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: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.95→41.7 Å / Num. obs: 28094 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 40.584 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 4.2 / Num. measured obs: 15394 / Num. unique all: 15394 / Num. unique obs: 1987 / % possible all: 95.8

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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: 1.95→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.87 / SU B: 5.6 / SU ML: 0.085 / SU R Cruickshank DPI: 0.146 / SU Rfree: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1430 5.1 %RANDOM
Rwork0.165 ---
obs0.167 28091 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.51 Å2 / Biso mean: 37.913 Å2 / Biso min: 25.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.74 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 49 169 2819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222782
X-RAY DIFFRACTIONr_angle_refined_deg1.5992.013790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2095360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99925.75899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79415484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.103157
X-RAY DIFFRACTIONr_chiral_restr0.110.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022052
X-RAY DIFFRACTIONr_nbd_refined0.2110.21272
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.213
X-RAY DIFFRACTIONr_mcbond_it0.971.51843
X-RAY DIFFRACTIONr_mcangle_it1.32622881
X-RAY DIFFRACTIONr_scbond_it2.4331089
X-RAY DIFFRACTIONr_scangle_it3.8424.5909
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 125 -
Rwork0.203 1880 -
all-2005 -
obs-2005 95.8 %
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)
13.38470.0180.10851.7623-0.06862.0270.0358-0.1882-0.16920.2267-0.0076-0.02230.23-0.0521-0.0282-0.0576-0.013-0.0386-0.16940.0148-0.141720.6954-1.677233.2029
22.2530.67770.44492.3432-0.56762.4601-0.04260.23210.0267-0.0992-0.0343-0.3550.03530.36180.0769-0.13890.0153-0.018-0.10580.0048-0.077132.57046.426320.2786
32.7377-0.13271.3442.7503-0.48786.61430.11380.2898-0.0731-0.3213-0.03490.02070.12670.0284-0.0789-0.107-0.0172-0.0119-0.1166-0.0005-0.123818.48548.8151-3.7398
43.19710.78351.32374.20810.84434.4140.0047-0.03210.0180.03340.12650.30620.0465-0.4384-0.1312-0.1007-0.0298-0.0069-0.0520.0617-0.15155.113417.9582-3.5259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 154
2X-RAY DIFFRACTION2A155 - 244
3X-RAY DIFFRACTION3A245 - 287
4X-RAY DIFFRACTION4A288 - 345

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