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- PDB-1w9g: Structure of ERH (Enhencer of Rudimentary Gene) -

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Basic information

Entry
Database: PDB / ID: 1w9g
TitleStructure of ERH (Enhencer of Rudimentary Gene)
ComponentsENHANCER OF RUDIMENTARY HOMOLOG
KeywordsERH(ENHANCER OF RUDIMENTARY HOMOLOG) / DCOH(DIMERIZATION COFACTOR OF HNF1)
Function / homology
Function and homology information


pyrimidine nucleoside metabolic process / methylosome / methyl-CpG binding / nucleobase-containing compound metabolic process / midbody / 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 / OTHER / Resolution: 2 Å
AuthorsWan, C. / Tempel, W. / Liu, Z. / Wang, B.-C. / Rose, R.B.
CitationJournal: Biochemistry / Year: 2005
Title: Structure of the Conserved Transcriptional Repressor Enhancer of Rudimentary Homolog
Authors: Wan, C. / Tempel, W. / Liu, Z. / Wang, B.-C. / Rose, R.B.
History
DepositionOct 13, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: 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
B: ENHANCER OF RUDIMENTARY HOMOLOG


Theoretical massNumber of molelcules
Total (without water)24,5482
Polymers24,5482
Non-polymers00
Water1,874104
1
A: ENHANCER OF RUDIMENTARY HOMOLOG


Theoretical massNumber of molelcules
Total (without water)12,2741
Polymers12,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENHANCER OF RUDIMENTARY HOMOLOG


Theoretical massNumber of molelcules
Total (without water)12,2741
Polymers12,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.480, 62.676, 48.564
Angle α, β, γ (deg.)90.00, 117.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENHANCER OF RUDIMENTARY HOMOLOG


Mass: 12273.927 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: MAMMALIAN GENE COLLECTION (MGC) IMAGE NUMBER 3507241 AND GENE BANK IDENTIFIER BC014301
Plasmid: PET24B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84090
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5
Details: 10% ISOPROPANOL, 20% PEG4000, 0.1M HEPES (PH7.5), pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→42.9 Å / Num. obs: 15585 / % possible obs: 95.3 % / Observed criterion σ(I): 2.8 / Redundancy: 2.5 % / Rmerge(I) obs: 0.03
Reflection shellResolution: 2→2.11 Å / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
MOSFLMdata scaling
SOLVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2→43.03 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.878 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 103 AND 104 OF EACH MONOMER ARE DISORDERD. PRO48B, SER49B, ILE50B ARE DISORDERD. THE SIDE CHAINS OF RESIDUES ARG42A AND B, ASN46B, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 103 AND 104 OF EACH MONOMER ARE DISORDERD. PRO48B, SER49B, ILE50B ARE DISORDERD. THE SIDE CHAINS OF RESIDUES ARG42A AND B, ASN46B, SER49A,ILE50A, THR51B, LYS12A AND B, GLU23B, LYS34B, LYS41A AND B, ASP75B, GLN77A AND B, GLN100A AND B, GLN101A AND B ARE DISORDERED AND OMITED FROM THIS MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.257 765 4.9 %RANDOM
Rwork0.196 ---
obs0.199 14786 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20.04 Å2
2--1.64 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 0 104 1703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0221629
X-RAY DIFFRACTIONr_bond_other_d0.0020.021439
X-RAY DIFFRACTIONr_angle_refined_deg2.3461.9522215
X-RAY DIFFRACTIONr_angle_other_deg1.14433343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.170.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021817
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02331
X-RAY DIFFRACTIONr_nbd_refined0.2290.2352
X-RAY DIFFRACTIONr_nbd_other0.260.21586
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0990.2930
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3450.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3210.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7281.51005
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.96721614
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7563624
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1514.5601
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 62
Rwork0.242 1040

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