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- PDB-4gvr: X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydro... -

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Basic information

Entry
Database: PDB / ID: 4gvr
TitleX-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase
ComponentsMethenyltetrahydromethanopterin cyclohydrolase
KeywordsHYDROLASE / methenyl-tetrahydromethanopterin / N5-formyl-tetrahydromethanopterin
Function / homology
Function and homology information


methenyltetrahydromethanopterin cyclohydrolase / methenyltetrahydromethanopterin cyclohydrolase activity / lactate oxidation / 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
Methenyltetrahydromethanopterin cyclohydrolase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsUpadhyay, V. / Demmer, U. / Warkentin, E. / Moll, J. / Shima, S. / Ermler, U.
CitationJournal: Biochemistry / Year: 2012
Title: Structure and catalytic mechanism of N(5),N(10)-methenyl-tetrahydromethanopterin cyclohydrolase.
Authors: Upadhyay, V. / Demmer, U. / Warkentin, E. / Moll, J. / Shima, S. / Ermler, U.
History
DepositionAug 31, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,6393
Polymers104,6393
Non-polymers00
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-41 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.540, 122.080, 79.390
Angle α, β, γ (deg.)90.00, 99.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1001 - 1314
2116B1001 - 1314
3116C1001 - 1314

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.315898, -0.59914, 0.73569), (0.571685, -0.498639, -0.651564), (0.757222, 0.62641, 0.185)-26.74818, 61.06065, 30.29628
3given(0.314443, 0.571923, 0.757648), (-0.596739, -0.501623, 0.62632), (0.73826, -0.64906, 0.183557)-49.34222, -4.3695, 53.86503

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Components

#1: Protein Methenyltetrahydromethanopterin cyclohydrolase / / Methenyl-H4MPT cyclohydrolase


Mass: 34879.637 Da / Num. of mol.: 3 / Mutation: E186Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_1935, mch / Plasmid: pET-24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS
References: UniProt: O28344, methenyltetrahydromethanopterin cyclohydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% (w/v) PEG 4000, 10% (v/v) Isopropanol, 0.1M Sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0001 Å
DetectorDate: Dec 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.52→48.17 Å / Num. all: 170753 / Num. obs: 164493

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASER2.1.4phasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QLM

1qlm


Resolution: 1.52→48.17 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.941 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23124 8252 5 %RANDOM
Rwork0.16425 ---
obs0.16754 156241 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.003 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20.17 Å2
2---0.16 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.52→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 0 740 8048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.027716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.97410525
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86351002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56326340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.329151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2941520
X-RAY DIFFRACTIONr_chiral_restr0.1450.21190
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215917
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_restr5.30937716
X-RAY DIFFRACTIONr_sphericity_free39.4155224
X-RAY DIFFRACTIONr_sphericity_bonded22.00658062
Refine LS restraints NCS

Ens-ID: 1 / Number: 2347 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.975
2BLOOSE POSITIONAL0.755
3CLOOSE POSITIONAL0.645
1ALOOSE THERMAL8.9310
2BLOOSE THERMAL11.410
3CLOOSE THERMAL9.6510
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 488 -
Rwork0.288 8691 -
obs--73.11 %

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