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- PDB-6zmg: PHAGE SAM LYASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE -

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Basic information

Entry
Database: PDB / ID: 6zmg
TitlePHAGE SAM LYASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
ComponentsChains: A
KeywordsLYASE / SAM lyase / S-adenosyl methionine / phage
Function / homologyPHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsGuo, X. / Kanchugal P, S. / Selmer, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationEvolution of new genes and proteins Sweden
Swedish Research Council2017-03827 Sweden
CitationJournal: Elife / Year: 2021
Title: Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family.
Authors: Guo, X. / Soderholm, A. / Kanchugal P, S. / Isaksen, G.V. / Warsi, O. / Eckhard, U. / Triguis, S. / Gogoll, A. / Jerlstrom-Hultqvist, J. / Aqvist, J. / Andersson, D.I. / Selmer, M.
History
DepositionJul 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700STRAND 6 IN SHEET AA1 IS CONTRIBUTED FROM A SYMMETRY-RELATED MOLECUL

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chains: A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8784
Polymers16,3031
Non-polymers5743
Water2,144119
1
A: Chains: A
hetero molecules

A: Chains: A
hetero molecules

A: Chains: A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,63312
Polymers48,9103
Non-polymers1,7239
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7420 Å2
ΔGint-39 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.473, 154.473, 154.473
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Space group name HallF4d23
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+1/4
#3: x+1/4,z+1/4,-y+1/4
#4: z+1/4,y+1/4,-x+1/4
#5: -z+1/4,y+1/4,x+1/4
#6: -y+1/4,x+1/4,z+1/4
#7: y+1/4,-x+1/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y+1/4,x+1/4,-z+1/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+1/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x,y+1/2,z+1/2
#26: x+1/4,-z+3/4,y+3/4
#27: x+1/4,z+3/4,-y+3/4
#28: z+1/4,y+3/4,-x+3/4
#29: -z+1/4,y+3/4,x+3/4
#30: -y+1/4,x+3/4,z+3/4
#31: y+1/4,-x+3/4,z+3/4
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y+1/4,x+3/4,-z+3/4
#44: -y+1/4,-x+3/4,-z+3/4
#45: z+1/4,-y+3/4,x+3/4
#46: -z+1/4,-y+3/4,-x+3/4
#47: -x+1/4,z+3/4,y+3/4
#48: -x+1/4,-z+3/4,-y+3/4
#49: x+1/2,y,z+1/2
#50: x+3/4,-z+1/4,y+3/4
#51: x+3/4,z+1/4,-y+3/4
#52: z+3/4,y+1/4,-x+3/4
#53: -z+3/4,y+1/4,x+3/4
#54: -y+3/4,x+1/4,z+3/4
#55: y+3/4,-x+1/4,z+3/4
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+3/4,x+1/4,-z+3/4
#68: -y+3/4,-x+1/4,-z+3/4
#69: z+3/4,-y+1/4,x+3/4
#70: -z+3/4,-y+1/4,-x+3/4
#71: -x+3/4,z+1/4,y+3/4
#72: -x+3/4,-z+1/4,-y+3/4
#73: x+1/2,y+1/2,z
#74: x+3/4,-z+3/4,y+1/4
#75: x+3/4,z+3/4,-y+1/4
#76: z+3/4,y+3/4,-x+1/4
#77: -z+3/4,y+3/4,x+1/4
#78: -y+3/4,x+3/4,z+1/4
#79: y+3/4,-x+3/4,z+1/4
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+3/4,x+3/4,-z+1/4
#92: -y+3/4,-x+3/4,-z+1/4
#93: z+3/4,-y+3/4,x+1/4
#94: -z+3/4,-y+3/4,-x+1/4
#95: -x+3/4,z+3/4,y+1/4
#96: -x+3/4,-z+3/4,-y+1/4
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

21A-416-

HOH

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Components

#1: Protein Chains: A


Mass: 16303.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): AI
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.6 M AMMONIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2016
RadiationMonochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.48→44.61 Å / Num. obs: 26719 / % possible obs: 99.7 % / Redundancy: 95 % / Biso Wilson estimate: 18.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.123 / Net I/σ(I): 32.44
Reflection shellResolution: 1.48→1.57 Å / Redundancy: 24.9 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 4522 / CC1/2: 0.774 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZM9

6zm9


Resolution: 1.48→44.59 Å / SU ML: 0.1226 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.5454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1717 1339 5.01 %random selection
Rwork0.1408 25378 --
obs0.1423 26717 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.95 Å2
Refinement stepCycle: LAST / Resolution: 1.48→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 36 119 1161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851120
X-RAY DIFFRACTIONf_angle_d1.10551522
X-RAY DIFFRACTIONf_chiral_restr0.0884171
X-RAY DIFFRACTIONf_plane_restr0.0062210
X-RAY DIFFRACTIONf_dihedral_angle_d17.6856435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.540.2491310.21492450X-RAY DIFFRACTION98.17
1.54-1.60.18491310.14452483X-RAY DIFFRACTION99.96
1.6-1.670.17981310.11532494X-RAY DIFFRACTION100
1.67-1.760.15631320.10682491X-RAY DIFFRACTION99.96
1.76-1.870.16371310.10922497X-RAY DIFFRACTION99.96
1.87-2.010.17421330.10592522X-RAY DIFFRACTION100
2.01-2.210.14971330.11072526X-RAY DIFFRACTION100
2.21-2.530.1471350.11932560X-RAY DIFFRACTION100
2.53-3.190.17311350.14972576X-RAY DIFFRACTION100
3.19-44.590.18081470.1682779X-RAY DIFFRACTION99.97

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