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- PDB-2nml: Crystal structure of HEF2/ERH at 1.55 A resolution -

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Basic information

Entry
Database: PDB / ID: 2nml
TitleCrystal structure of HEF2/ERH at 1.55 A resolution
ComponentsEnhancer of rudimentary homolog
KeywordsTRANSCRIPTION / HEF2/ERH fold / pseudo beta barrel / interaction network / cell cycle
Function / homology
Function and homology information


pyrimidine nucleoside metabolic process / methylosome / methyl-CpG binding / nucleobase-containing compound metabolic process / midbody / cell cycle / RNA binding / nucleus
Similarity search - Function
ERH-like fold / Enhancer of rudimentary / Enhancer of rudimentary signature. / Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Enhancer of rudimentary homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJin, T.C. / Guo, F. / Serebriiskii, I.G. / Howard, A.J. / Zhang, Y.Z.
CitationJournal: Proteins / Year: 2007
Title: A 1.55 A resolution X-ray crystal structure of HEF2/ERH and insights into its transcriptional and cell-cycle interaction networks.
Authors: Jin, T. / Guo, F. / Serebriiskii, I.G. / Howard, A. / Zhang, Y.Z.
History
DepositionOct 21, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionOct 31, 2006ID: 2I4F
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enhancer of rudimentary homolog


Theoretical massNumber of molelcules
Total (without water)12,2741
Polymers12,2741
Non-polymers00
Water2,342130
1
A: Enhancer of rudimentary homolog

A: Enhancer of rudimentary homolog


Theoretical massNumber of molelcules
Total (without water)24,5482
Polymers24,5482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)53.739, 53.739, 67.448
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: y, x, -z.

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Components

#1: Protein Enhancer of rudimentary homolog / Enhancer of Filamentation 2 / HEF2 / ERH


Mass: 12273.927 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERH / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), B834(DE3) / References: UniProt: P84090
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, isopropanol, trisodium citrate dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11
SYNCHROTRONAPS 17-ID20.95000, 0.97950, 0.97900
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.951
30.97951
40.9791
Reflection

D res low: 50 Å / Redundancy: 7.2 %

IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
116.2608090.0620.992.29847983.2
214.9599910.0611.012.32830784.5
314.9606760.0650.992.31842584.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.935085.910.0621.0117.3
3.924.9381.810.0510.9097.3
3.423.9211.910.0520.9985.2
3.113.4294.810.0550.9367.4
2.893.1195.210.0641.0467.3
2.722.8995.210.0750.9677.4
2.582.7295.310.0911.0297.3
2.472.5895.910.120.9727.4
2.372.4796.510.1531.017.1
2.292.3779.910.4681.0246.1
55087.520.0570.9377.3
3.97588.520.0461.0217.3
3.473.970.221
3.153.4792.820.0561.0567
2.923.1594.820.0651.0257.4
2.752.9295.520.0810.9597.3
2.612.7595.720.1091.0337.3
2.52.619620.1540.9887.3
2.42.596.220.191.0177.3
2.322.496.120.5961.0166.7
4.985086.330.0651.0097.3
3.954.9886.330.0520.947.4
3.453.956.230.0530.9343.8
3.133.4594.330.0580.9997.3
2.913.139530.0661.0017.4
2.742.9195.930.081.0017.3
2.62.7495.630.1020.9937.3
2.492.696.130.1380.9387.3
2.392.499630.1730.9757.3
2.312.3994.330.5511.0556.4
ReflectionResolution: 1.55→38.32 Å / Num. obs: 16613 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.051 / Χ2: 0.986 / Net I/σ(I): 15
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.606 / Num. unique all: 1570 / Χ2: 0.964 / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→38.32 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 786 4.7 %RANDOM
Rwork0.198 ---
all0.2 15983 --
obs0.2 15983 94.8 %-
Solvent computationBsol: 85.441 Å2
Displacement parametersBiso mean: 28.268 Å2
Baniso -1Baniso -2Baniso -3
1-0.719 Å2-0.013 Å20 Å2
2--0.719 Å20 Å2
3----1.437 Å2
Refine analyzeLuzzati coordinate error obs: 0.181 Å
Refinement stepCycle: LAST / Resolution: 1.55→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 0 130 946
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.044
LS refinement shellResolution: 1.55→1.61 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.29 70 -
Rwork0.271 --
obs-1269 85.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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