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- PDB-4fio: Crystal Structure of Methenyltetrahydromethanopterin Cyclohydrola... -

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Basic information

Entry
Database: PDB / ID: 4fio
TitleCrystal Structure of Methenyltetrahydromethanopterin Cyclohydrolase from Methanobrevibacter ruminantium
ComponentsMethenyltetrahydromethanopterin cyclohydrolase
KeywordsHYDROLASE / methanogenesis / hydrolysis
Function / homology
Function and homology information


methenyltetrahydromethanopterin cyclohydrolase / methenyltetrahydromethanopterin cyclohydrolase activity / methanogenesis, from carbon dioxide / one-carbon metabolic process / cytoplasm
Similarity search - Function
Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 1 / Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 1 / Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 / Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 / Methenyltetrahydromethanopterin cyclohydrolase / Cyclohydrolase (MCH) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHYL ACETATE / ISOPROPYL ALCOHOL / Methenyltetrahydromethanopterin cyclohydrolase
Similarity search - Component
Biological speciesMethanobrevibacter ruminantium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsCarbone, V. / Schofield, L.R. / Beattie, A.K. / Sutherland-Smith, A.J. / Ronimus, R.S.
CitationJournal: Proteins / Year: 2013
Title: The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from Methanobrevibacter ruminantium.
Authors: Carbone, V. / Schofield, L.R. / Beattie, A.K. / Sutherland-Smith, A.J. / Ronimus, R.S.
History
DepositionJun 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 13, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methenyltetrahydromethanopterin cyclohydrolase
B: Methenyltetrahydromethanopterin cyclohydrolase
C: Methenyltetrahydromethanopterin cyclohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,5828
Polymers113,2263
Non-polymers3565
Water19,2941071
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-17 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.370, 74.855, 74.816
Angle α, β, γ (deg.)120.06, 100.01, 98.28
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.849807, 0.447625, 0.278318), (-0.03978, -0.472052, 0.880673), (0.525591, -0.759473, -0.383347)-0.07427, -37.32638, 20.03291
3given(0.842348, -0.051761, 0.536443), (0.453916, -0.468457, -0.757963), (0.290534, 0.881969, -0.371109)12.11939, -36.55814, -21.27586

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Components

#1: Protein Methenyltetrahydromethanopterin cyclohydrolase / Methenyl-H4MPT cyclohydrolase


Mass: 37741.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter ruminantium (archaea)
Strain: ATCC 35063 / DSM 1093 / JCM 13430 / M1 / Gene: mch, mru_1619 / Plasmid: pET151D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: D3E4S5, methenyltetrahydromethanopterin cyclohydrolase
#2: Chemical ChemComp-EEE / ETHYL ACETATE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1071 / 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: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl, 30% (w/v) PEG 4000 and 3% (v/v) isopropanol, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953691
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2011
RadiationMonochromator: SI VORTEX-ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953691 Å / Relative weight: 1
ReflectionResolution: 1.37→19.88 Å / Num. obs: 184543 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Net I/σ(I): 17.3
Reflection shellResolution: 1.37→1.44 Å / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.606 / % possible all: 79.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLM

1qlm


Resolution: 1.37→19.88 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.612 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.175 9299 5 %RANDOM
Rwork0.13 ---
obs0.132 175155 93.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20.72 Å2-1.55 Å2
2---0.44 Å24.45 Å2
3----1.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.144 Å
Refinement stepCycle: LAST / Resolution: 1.37→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7144 0 24 1071 8239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.027577
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2971.98710330
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9451037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40726.312301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.995151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.144159
X-RAY DIFFRACTIONr_chiral_restr0.1640.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215698
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_restr8.44137577
X-RAY DIFFRACTIONr_sphericity_free19.255262
X-RAY DIFFRACTIONr_sphericity_bonded10.75758223
LS refinement shellResolution: 1.37→1.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 507 -
Rwork0.236 9303 -
obs--67.33 %

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