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- PDB-9zrf: Crystal structure of macrodomain from Venezuelan equine encephali... -

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Basic information

Entry
Database: PDB / ID: 9zrf
TitleCrystal structure of macrodomain from Venezuelan equine encephalitis virus in complex with Adenosine diphosphate ribose
ComponentsPolyprotein P1234
KeywordsVIRAL PROTEIN / MACRO DOMAIN / Venezuelan equine encephalitis virus / alpha virus / Adenosine diphosphate ribose
Function / homologyADENOSINE-5-DIPHOSPHORIBOSE / Chem-AR6 / :
Function and homology information
Biological speciesVenezuelan equine encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsChang, C. / Endre, M. / Stols, L. / Kim, Y. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Crystal structure of macrodomain from Venezuelan equine encephalitis virus in complex with Adenosine diphosphate ribose
Authors: Chang, C. / Endre, M. / Stols, L. / Kim, Y. / Joachimiak, A.
History
DepositionDec 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyprotein P1234
B: Polyprotein P1234
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3336
Polymers35,0962
Non-polymers2,2374
Water5,999333
1
A: Polyprotein P1234
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6673
Polymers17,5481
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyprotein P1234
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6673
Polymers17,5481
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.539, 39.882, 55.154
Angle α, β, γ (deg.)77.84, 71.57, 62.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Polyprotein P1234 / Non-structural polyprotein


Mass: 17547.873 Da / Num. of mol.: 2 / Fragment: Macrodomain, residues 1330-1489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Gene: NSP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1JQW9
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 40410 / % possible obs: 89.2 % / Redundancy: 2.8 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.049 / Rrim(I) all: 0.086 / Χ2: 0.828 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.532.20.33614690.8140.9470.2550.4240.67762.5
1.53-1.552.30.34315800.8030.9440.2620.4340.73772.3
1.55-1.582.30.33619400.8320.9530.2540.4240.72384.4
1.58-1.622.60.35220160.8630.9620.2570.4380.71490.7
1.62-1.652.80.3621620.840.9550.2520.4410.70893.8
1.65-1.692.90.35420940.8310.9530.2460.4330.72493.7
1.69-1.7330.31121810.8690.9640.2150.3790.77494.8
1.73-1.7830.27921100.8890.970.1910.340.73693.9
1.78-1.832.90.24421270.8940.9720.1710.30.80494.4
1.83-1.892.70.20521460.9270.9810.1480.2540.91593.3
1.89-1.962.90.20221070.9270.9810.140.2470.92793.7
1.96-2.042.90.14820760.9580.9890.1050.183192.1
2.04-2.132.80.12420520.9690.9920.0870.1521.10891.7
2.13-2.2430.11121230.9640.9910.0770.1361.08693
2.24-2.382.90.0920620.9760.9940.0630.1110.97891.1
2.38-2.5630.07220800.980.9950.050.0880.91892.4
2.56-2.822.90.05621380.990.9970.0390.0690.84193
2.82-3.232.70.04420530.9910.9980.0320.0550.73991.2
3.23-4.072.50.03917700.9920.9980.0290.0490.70778
4.07-503.10.03721240.9930.9980.0250.0440.54894

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→35.31 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 1790 4.86 %
Rwork0.1607 --
obs0.1637 36849 80.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 72 333 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052735
X-RAY DIFFRACTIONf_angle_d0.7683746
X-RAY DIFFRACTIONf_dihedral_angle_d14.1921073
X-RAY DIFFRACTIONf_chiral_restr0.073438
X-RAY DIFFRACTIONf_plane_restr0.005474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.530.3564470.24151084X-RAY DIFFRACTION32
1.53-1.580.3326900.18791646X-RAY DIFFRACTION49
1.58-1.630.25381190.19432150X-RAY DIFFRACTION65
1.63-1.690.27651360.18912711X-RAY DIFFRACTION81
1.69-1.760.25571550.16973005X-RAY DIFFRACTION89
1.76-1.840.2371630.18053075X-RAY DIFFRACTION92
1.84-1.930.23881500.18263106X-RAY DIFFRACTION93
1.93-2.050.21911510.17683103X-RAY DIFFRACTION92
2.05-2.210.23631540.15883118X-RAY DIFFRACTION92
2.21-2.440.22181760.15973045X-RAY DIFFRACTION91
2.44-2.790.22211570.16043095X-RAY DIFFRACTION93
2.79-3.510.2421420.15293094X-RAY DIFFRACTION92
3.51-35.310.16521500.13562827X-RAY DIFFRACTION84

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