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

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Basic information

Entry
Database: PDB / ID: 9zre
TitleCrystal structure of macrodomain from Venezuelan equine encephalitis virus
ComponentsPolyprotein P1234
KeywordsVIRAL PROTEIN / MACRO DOMAIN / Venezuelan equine encephalitis virus / alpha virus
Function / homology:
Function and homology information
Biological speciesVenezuelan equine encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
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)34,7644
Polymers34,6932
Non-polymers712
Water7,062392
1
A: Polyprotein P1234
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3822
Polymers17,3471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyprotein P1234
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3822
Polymers17,3471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.543, 98.467, 39.514
Angle α, β, γ (deg.)90.00, 118.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyprotein P1234 / Non-structural polyprotein


Mass: 17346.691 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Lithium chloride, HEPES, PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 60073 / % possible obs: 92.1 % / Redundancy: 5.5 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.066 / Rrim(I) all: 0.163 / Χ2: 0.949 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.3-1.322.80.49714070.4360.7790.2850.5790.75143.4
1.32-1.3530.44218000.8670.9640.2330.5040.79155.4
1.35-1.373.40.43924270.8360.9540.2270.4980.77674.4
1.37-1.440.44829060.8620.9620.2230.5030.90288.8
1.4-1.434.70.45230650.8860.9690.210.5010.89895.8
1.43-1.465.30.37432070.9450.9860.1660.4110.97797.6
1.46-1.55.50.34731650.9270.9810.1550.3811.01597.7
1.5-1.545.70.32232300.9430.9850.1420.3531.00299.2
1.54-1.595.70.28332030.930.9820.1260.3111.04998.2
1.59-1.645.80.24732200.9080.9760.1120.2710.90998.6
1.64-1.75.80.22332020.9370.9840.1010.2450.86498.6
1.7-1.765.80.20932040.9610.990.0950.230.85199.1
1.76-1.845.50.21832280.940.9840.1020.2410.93899
1.84-1.945.80.20832320.8920.9710.0950.230.98999
1.94-2.066.30.17532380.9690.9920.0750.1910.97699.2
2.06-2.226.40.16532160.9670.9920.070.1791.04898.9
2.22-2.456.30.14832590.9420.9850.0640.1611.05599.6
2.45-2.86.30.13732970.7480.9250.0610.1510.97799.7
2.8-3.535.90.11932510.9530.9880.0540.1310.94599.7
3.53-506.80.12233160.7170.9140.0540.1340.85299.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→49.23 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.667 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17729 2731 5 %RANDOM
Rwork0.14689 ---
obs0.14853 51833 83.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.078 Å2
Baniso -1Baniso -2Baniso -3
1-4.35 Å20 Å2-1.08 Å2
2---2.71 Å2-0 Å2
3----1.65 Å2
Refinement stepCycle: 1 / Resolution: 1.3→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 2 392 2833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122605
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162522
X-RAY DIFFRACTIONr_angle_refined_deg1.281.8183544
X-RAY DIFFRACTIONr_angle_other_deg0.4711.7775829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.841513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31410457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8391.4961351
X-RAY DIFFRACTIONr_mcbond_other2.8321.4961351
X-RAY DIFFRACTIONr_mcangle_it4.3072.691708
X-RAY DIFFRACTIONr_mcangle_other4.3082.6931709
X-RAY DIFFRACTIONr_scbond_it3.4461.7111254
X-RAY DIFFRACTIONr_scbond_other3.4371.7081253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3013.0431837
X-RAY DIFFRACTIONr_long_range_B_refined13.24924.793036
X-RAY DIFFRACTIONr_long_range_B_other10.57619.262917
X-RAY DIFFRACTIONr_rigid_bond_restr2.55735127
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 59 -
Rwork0.239 900 -
obs--19.9 %

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