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- PDB-6znb: PHAGE SAM LYASE IN APO STATE -

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Basic information

Entry
Database: PDB / ID: 6znb
TitlePHAGE SAM LYASE IN APO STATE
ComponentsPhage SAM lyase Svi3-3
KeywordsLYASE / SAM lyase / S-adenosyl methionine / phage
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesBacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEckhard, U. / 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 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Phage SAM lyase Svi3-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4933
Polymers16,3031
Non-polymers1902
Water543
1
AA: Phage SAM lyase Svi3-3
hetero molecules

AA: Phage SAM lyase Svi3-3
hetero molecules

AA: Phage SAM lyase Svi3-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4809
Polymers48,9103
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation54_555z,-x,-y1
Buried area6360 Å2
ΔGint-45 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.477, 158.477, 158.477
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
11AA-201-

PO4

21AA-201-

PO4

31AA-302-

HOH

41AA-303-

HOH

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Components

#1: Protein Phage SAM lyase Svi3-3


Mass: 16303.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Escherichia coli BL21 (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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0722 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.8→39.62 Å / Num. obs: 4409 / % possible obs: 97.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 71.99 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.125 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 634 / CC1/2: 0.61 / Rrim(I) all: 0.939 / % possible all: 98.5

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Processing

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

6zm9


Resolution: 2.8→39.62 Å / SU ML: 0.2331 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.826
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2737 221 5.03 %
Rwork0.2324 4175 -
obs0.2345 4396 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.62 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms979 0 10 3 992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025998
X-RAY DIFFRACTIONf_angle_d0.45991345
X-RAY DIFFRACTIONf_chiral_restr0.048154
X-RAY DIFFRACTIONf_plane_restr0.0026172
X-RAY DIFFRACTIONf_dihedral_angle_d2.9789594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.530.34191090.30782062X-RAY DIFFRACTION98.46
3.53-39.620.25051120.2072113X-RAY DIFFRACTION94.48
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)
16.388515928341.1591641598-1.355709805731.70040717836-0.6997790718010.750356156866-0.656919929861-0.94034369173-0.355871807816-0.1221122064620.119627341375-0.519665583428-0.5551127955490.3441684017840.4967979938570.698615432370.00987424281770.01956207884580.528450782838-0.02884845298590.65660201315831.681652568-19.003073934533.1547683337
25.24360166194-0.3553012270980.4523100315474.13240146729-0.1984137203093.98510401817-0.0976692562484-0.1739058664590.9454470706020.1105173353980.002394199130320.366956209484-0.294925645098-0.02290013141420.1527505645260.472727158695-0.02505880561370.03546866323090.534981423836-0.1481755414790.56094791920312.0952806365-13.120736164233.0950870858
35.908324089176.022065381410.6134922397676.92384164788-1.073443230085.080106866710.09925229482920.9640827762190.3043602428450.06247703312911.075793165871.093028134460.5754645760530.768154621781-0.4344016643460.5607102975280.1166791483060.1194446352420.3535248002210.02280799958030.79860863538710.2359581633-26.241089255524.8047000611
44.38275741358-1.073463093022.28977811181.55617617023-0.6290642948954.62126571835-0.0786169031309-0.6129340084920.435142728021-0.178243647981-0.505008896554-0.2470286648790.123232939568-0.4370651548570.4698884885770.631353652989-0.1317257935090.1666159014710.69340644695-0.0359355225580.60598864979619.9485762813-19.704286222533.0811974468
58.26977435368-0.1223466587750.5994345983065.11422888901-0.3132929700213.27673627631-0.372282777355-1.960516655180.2443977515790.8288900028690.1815330693290.2203458316550.1899560228080.2575533311730.0975551633160.6065964857740.05291559214760.1006820208490.812068098117-0.15002332960.50358983399815.563707676-19.601973310242.2505228609
68.77552852164-2.43262458074-0.8300299868546.533195079010.4964980984522.61327001112-0.597483863697-0.7434617136270.2675244388630.1626997435740.504321135374-0.4456730073060.376065421160.364002294077-0.0304994084750.5930796136520.01378346333130.1389401872430.588720910858-0.02431201371720.60288685735418.6108119985-27.513499540937.4315326019
76.235377793111.72025899511-4.656275357875.87334557909-3.89537836434.74431745548-1.058669476870.428878074148-0.8288803731280.9180974037580.425503652838-0.399188429440.260396248514-0.4123056854010.3229389366811.203737771620.192620550740.05720376658160.809983125096-0.198389334680.784262828617-1.95886453843-28.250793315542.4806725792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'AA' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'AA' and (resid 19 through 49 )
3X-RAY DIFFRACTION3chain 'AA' and (resid 50 through 66 )
4X-RAY DIFFRACTION4chain 'AA' and (resid 67 through 83 )
5X-RAY DIFFRACTION5chain 'AA' and (resid 84 through 102 )
6X-RAY DIFFRACTION6chain 'AA' and (resid 103 through 124 )
7X-RAY DIFFRACTION7chain 'AA' and (resid 125 through 129 )

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