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

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Basic information

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


methenyltetrahydromethanopterin cyclohydrolase / methenyltetrahydromethanopterin cyclohydrolase activity / lactate metabolic process / 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
Chem-F4M / Methenyltetrahydromethanopterin cyclohydrolase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: Methenyltetrahydromethanopterin cyclohydrolase
B: Methenyltetrahydromethanopterin cyclohydrolase
C: Methenyltetrahydromethanopterin cyclohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4444
Polymers104,6393
Non-polymers8051
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-42 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.900, 108.990, 114.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1001 - 1315
2116B1001 - 1315
3116C1001 - 1315

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.393053, -0.917145, 0.065988), (-0.319822, -0.069074, 0.944956), (-0.862104, -0.392522, -0.320473)-9.80932, -52.17581, 59.08779
3given(0.379679, -0.318809, -0.86845), (-0.922679, -0.062371, -0.380491), (0.067138, 0.945765, -0.317839)38.35057, 10.06296, 68.88309

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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: Chemical ChemComp-F4M / 1-[4-({(1R)-1-[(6S,7R)-2-amino-5-formyl-7-methyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]ethyl}amino)phenyl]-1-deoxy-5 -O-{5-O-[(R)-{[(1R)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol / N5-formyl-tetrahydromethanopterin


Mass: 804.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H45N6O17P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8% (w/v) PEG 4000, 0.1M ammonium acetate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.214 Å
DetectorDate: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214 Å / Relative weight: 1
ReflectionResolution: 1.75→43.402 Å / Num. all: 116728 / Num. obs: 108423

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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: 1.75→43.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.204 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22421 5423 5 %RANDOM
Rwork0.18718 ---
obs0.18902 103000 92.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.853 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 55 510 7873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.027695
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.97810490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22225.929339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.014151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1931521
X-RAY DIFFRACTIONr_chiral_restr0.1520.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215876
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2330 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.615
2BLOOSE POSITIONAL0.655
3CLOOSE POSITIONAL1.025
1ALOOSE THERMAL6.710
2BLOOSE THERMAL6.2710
3CLOOSE THERMAL4.4210
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 304 -
Rwork0.247 5802 -
obs--73.16 %

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