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- PDB-9dzs: Acanthamoeba Polyphaga Mimivirus R699 -

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Basic information

Entry
Database: PDB / ID: 9dzs
TitleAcanthamoeba Polyphaga Mimivirus R699
ComponentsR699
KeywordsVIRAL PROTEIN / R699
Function / homologyPLOD GT domain / procollagen-lysine 5-dioxygenase activity / : / : / URIDINE-5'-DIPHOSPHATE / Uncharacterized protein R699
Function and homology information
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRichards, S.J. / Buhlheller, C. / 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
DepositionOct 17, 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

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Assembly

Deposited unit
A: R699
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9615
Polymers53,3171
Non-polymers6434
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.041, 71.481, 72.626
Angle α, β, γ (deg.)90.000, 123.178, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein R699


Mass: 53317.438 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Protein/cofactor mix: 12mg/ml R699, 10mM MnCl2, 10mM UDP glucose, 50% glycerol. Mother liquor: 0.18 M Ammonium chloride, 18% (w/v) PEG 3350, 4% v/v 1-Propanol. 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: Jul 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→60.79 Å / Num. obs: 349711 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 18358 / CC1/2: 0.921 / % possible all: 98.5

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Processing

Software
NameVersionClassification
DIALS3.8.0data collection
xia23.8.0data reduction
Aimless0.7.8data scaling
PHENIX1.20.1phasing
PHASER2.8.3phasing
Coot0.9.8.92model building
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→57.98 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.539 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.1 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1953 2462 4.86 %
Rwork0.1706 48194 -
all0.172 --
obs-50656 99.166 %
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: 20.727 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å2-1.188 Å2
2---0.387 Å20 Å2
3----0.808 Å2
Refinement stepCycle: LAST / Resolution: 1.75→57.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3605 0 38 291 3934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123766
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.8265094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8775447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.079515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1710668
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.80510190
X-RAY DIFFRACTIONr_chiral_restr0.1190.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022873
X-RAY DIFFRACTIONr_nbd_refined0.2010.21651
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2245
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.215
X-RAY DIFFRACTIONr_mcbond_it1.8921.8151767
X-RAY DIFFRACTIONr_mcangle_it2.9793.2542209
X-RAY DIFFRACTIONr_scbond_it2.8832.0791999
X-RAY DIFFRACTIONr_scangle_it4.5933.6772881
X-RAY DIFFRACTIONr_lrange_it6.21623.1115837
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
1.75-1.7950.2552330.24134750.24237600.9340.93398.6170.223
1.795-1.8450.2311790.21634520.21636380.9480.95199.80760.198
1.845-1.8980.2041800.19533920.19535810.960.96499.74870.181
1.898-1.9560.2281460.18433210.18634740.9610.97199.79850.168
1.956-2.020.2091580.17431830.17533540.9710.97599.61240.162
2.02-2.0910.2211770.17330430.17632550.9680.97898.92470.164
2.091-2.170.1891400.17729280.17731180.9710.97998.39640.168
2.17-2.2580.2121390.17327920.17530160.970.98197.18170.165
2.258-2.3590.2171290.17127660.17328980.9670.98199.89650.166
2.359-2.4740.207860.17326750.17427630.9710.9899.92760.169
2.474-2.6070.228990.16125300.16326360.9730.98399.73440.16
2.607-2.7650.1981040.15923950.16125070.9730.98599.68090.159
2.765-2.9550.161810.1622430.1623290.980.98499.78530.166
2.955-3.1920.2021520.15619860.15922060.9730.98596.91750.166
3.192-3.4950.1961320.15218760.15520090.9750.98699.95020.165
3.495-3.9060.178760.1517470.15118240.980.98799.94520.166
3.906-4.5070.1621050.15115070.15216230.9850.98799.32220.172
4.507-5.5110.15680.16212900.16113690.9880.98699.19650.189
5.511-7.7590.218540.2349970.23310790.9820.97897.4050.275
7.759-57.980.191240.1995960.1996250.9840.9899.20.236

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