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- PDB-9e92: Acanthamoeba Polyphaga Mimivirus R699 -

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Basic information

Entry
Database: PDB / ID: 9.0E+92
TitleAcanthamoeba Polyphaga Mimivirus R699
ComponentsR699
KeywordsVIRAL PROTEIN / R699
Function / homologyprocollagen-lysine 5-dioxygenase activity / : / beta-D-glucopyranose / beta-D-galactopyranose / : / URIDINE-5'-DIPHOSPHATE / Uncharacterized protein R699
Function and homology information
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBuhlheller, C. / Richards, S.J. / Kim, J.S. / Chen, T. / Wu, J. / Guo, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R00CA225633 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R37CA278989 United States
CitationJournal: To Be Published
Title: Acanthamoeba Polyphaga Mimivirus R699
Authors: Richards, S.J. / Buhlheller, C. / Kim, J.S. / Chen, T. / Wu, J. / Guo, H.
History
DepositionNov 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R699
B: R699
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,97613
Polymers106,6352
Non-polymers2,34111
Water15,907883
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.153, 124.998, 72.757
Angle α, β, γ (deg.)90.000, 118.295, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 9 - 455 / Label seq-ID: 12 - 458

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein R699


Mass: 53317.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UNV6

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Sugars , 3 types, 7 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 887 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 883 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Protein/substrate/cofactor mix: 28 mg/ml R699, 10 mM UDP glucose, 10 mM MnCl2, 0.15 g/ml glucose, 0.15 g/ml galactose. Mother liquor: 0.1 M HEPES pH 7, 10% (w/v) PEG 6000. The ratio of mix ...Details: Protein/substrate/cofactor mix: 28 mg/ml R699, 10 mM UDP glucose, 10 mM MnCl2, 0.15 g/ml glucose, 0.15 g/ml galactose. Mother liquor: 0.1 M HEPES pH 7, 10% (w/v) PEG 6000. The ratio of mix and mother liquor was at 1:1.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→62.5 Å / Num. obs: 171464 / % possible obs: 98.4 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.3
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 49803 / CC1/2: 0.857

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALS3.8.0data collection
xia23.8.0data reduction
Aimless0.7.8data scaling
PHENIX1.20.1phasing
PHASER2.8.3phasing
Coot0.9.8.93model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→60.965 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.167 / SU B: 1.305 / SU ML: 0.048 / Average fsc free: 0.9728 / Average fsc work: 0.9794 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.066
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.189 8633 5.041 %
Rwork0.1657 162639 -
all0.167 --
obs-171272 98.733 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.197 Å20 Å2-0.376 Å2
2--1.682 Å20 Å2
3----0.933 Å2
Refinement stepCycle: LAST / Resolution: 1.5→60.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7306 0 147 883 8336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0127845
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167309
X-RAY DIFFRACTIONr_angle_refined_deg1.81.8310647
X-RAY DIFFRACTIONr_angle_other_deg0.6241.77616884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7625938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.853535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.091101401
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.90610392
X-RAY DIFFRACTIONr_chiral_restr0.0980.21155
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021863
X-RAY DIFFRACTIONr_nbd_refined0.2230.21247
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.26163
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23688
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2524
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.216
X-RAY DIFFRACTIONr_nbd_other0.1460.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.227
X-RAY DIFFRACTIONr_mcbond_it1.8441.8053643
X-RAY DIFFRACTIONr_mcbond_other1.8421.8043643
X-RAY DIFFRACTIONr_mcangle_it2.6653.254580
X-RAY DIFFRACTIONr_mcangle_other2.6653.254581
X-RAY DIFFRACTIONr_scbond_it3.1032.1294202
X-RAY DIFFRACTIONr_scbond_other3.1022.1294203
X-RAY DIFFRACTIONr_scangle_it4.6973.7646055
X-RAY DIFFRACTIONr_scangle_other4.6963.7646056
X-RAY DIFFRACTIONr_lrange_it5.88121.5828730
X-RAY DIFFRACTIONr_lrange_other5.80620.4928554
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.0514726
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.091390.05008
12AX-RAY DIFFRACTIONLocal ncs0.091390.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.2876360.263121040.264128490.9530.95899.15170.242
1.539-1.5810.2636050.226118370.228124750.9580.96899.73550.202
1.581-1.6270.2245860.209115240.21121430.9670.97299.72820.183
1.627-1.6770.2155980.19110670.191117270.970.97799.47130.166
1.677-1.7320.2125120.179107670.181114410.9710.97998.5840.155
1.732-1.7930.1945910.168101990.17110320.9760.98297.80640.147
1.793-1.860.2035370.17695460.178106820.9680.97894.39240.156
1.86-1.9360.1964640.16497180.166102210.9760.98399.61840.147
1.936-2.0220.2045160.16993660.1798880.9730.98399.93930.155
2.022-2.1210.1924750.16788450.16893650.9770.98499.51950.157
2.121-2.2350.1935020.16484140.16589700.9780.98599.3980.157
2.235-2.3710.1824460.15580050.15785010.9810.98699.41180.152
2.371-2.5340.1823850.15273550.15379440.9790.98697.4320.152
2.534-2.7370.1772950.15268080.15374160.980.98695.77940.156
2.737-2.9970.1863040.15865340.15968380.9790.9851000.166
2.997-3.350.1873560.15958090.16161760.9770.98699.82190.173
3.35-3.8660.1712940.15451810.15554940.9840.98799.65420.173
3.866-4.7310.1422490.13342840.13346260.9890.99197.98960.158
4.731-6.670.2021780.1833280.18236040.9850.98897.28080.211
6.67-60.9650.2061030.20119220.20120290.9790.97999.80290.249

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