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- PDB-4m7r: Crystal structure of the N-terminal methyltransferase-like domain... -

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Basic information

Entry
Database: PDB / ID: 4m7r
TitleCrystal structure of the N-terminal methyltransferase-like domain of anamorsin
ComponentsAnamorsin
KeywordsAPOPTOSIS / ROSSMANN FOLD
Function / homology
Function and homology information


Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly / hemopoiesis / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / apoptotic process / nucleolus ...Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly / hemopoiesis / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / apoptotic process / nucleolus / negative regulation of apoptotic process / mitochondrion / nucleoplasm / cytoplasm
Similarity search - Function
Anamorsin, C-terminal / : / Anamorsin, N-terminal / Anamorsin / Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsSong, G. / Liu, Z.-J.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of the N-terminal methyltransferase-like domain of anamorsin.
Authors: Song, G. / Cheng, C. / Li, Y. / Shaw, N. / Xiao, Z.C. / Liu, Z.J.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anamorsin
B: Anamorsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7673
Polymers42,5662
Non-polymers2011
Water5,062281
1
A: Anamorsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4842
Polymers21,2831
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anamorsin


Theoretical massNumber of molelcules
Total (without water)21,2831
Polymers21,2831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.508, 79.508, 101.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Anamorsin / Cytokine-induced apoptosis inhibitor 1 / Fe-S cluster assembly protein DRE2 homolog


Mass: 21283.066 Da / Num. of mol.: 2 / Fragment: methyltransferase-like domain, UNP residues 1-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIAPIN1, CUA001, PRO0915 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6FI81
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.5
Details: 0.17M sodium acetate trihydrate, 0.085M sodium cacodylate pH6.5, 25% PEG 8000, 15% Glycerol, EVAPORATION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2008
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromatoR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30.43 Å / Num. all: 33762 / Num. obs: 33762 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.7 % / Biso Wilson estimate: 21.95 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 42.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value
1.8-1.837.50.514.0916660.51
1.83-1.869.10.4694.516860.469
1.86-1.910.70.398717150.396
1.9-1.9411.10.319.1716510.31
1.94-1.9811.20.25511.4416930.255
1.98-2.0311.20.2113.316860.21

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: dev_1372)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.801→30.426 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8364 / SU ML: 0.2 / σ(F): 1.33 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1708 5.07 %RANDOM
Rwork0.1874 ---
all-33762 --
obs-33703 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.73 Å2 / Biso mean: 28.2786 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: LAST / Resolution: 1.801→30.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 1 281 2994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072740
X-RAY DIFFRACTIONf_angle_d1.0313708
X-RAY DIFFRACTIONf_dihedral_angle_d13.7991018
X-RAY DIFFRACTIONf_chiral_restr0.069442
X-RAY DIFFRACTIONf_plane_restr0.005482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8011-1.85410.29351490.242426602809
1.8541-1.91390.25561430.229926402783
1.9139-1.98230.25431350.207526752810
1.9823-2.06170.25021290.201426582787
2.0617-2.15550.25531780.203926362814
2.1555-2.26910.25071460.186826652811
2.2691-2.41120.26821460.19626512797
2.4112-2.59730.21911450.205226552800
2.5973-2.85850.23751280.196926782806
2.8585-3.27170.21631290.179626782807
3.2717-4.12040.20851370.16626862823
4.1204-30.43020.18941430.173327132856
Refinement TLS params.Method: refined / Origin x: 39.2964 Å / Origin y: -13.8878 Å / Origin z: -17.3673 Å
111213212223313233
T0.1701 Å20.0279 Å20.0069 Å2-0.1017 Å2-0.0082 Å2--0.1315 Å2
L3.6672 °20.5581 °20.5591 °2-0.1072 °20.1075 °2--0.3645 °2
S-0.0245 Å °0.1717 Å °-0.0843 Å °-0.0513 Å °0.0248 Å °-0.0328 Å °0.0626 Å °0.0674 Å °0.0039 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 1116
2X-RAY DIFFRACTION1allB12 - 188
3X-RAY DIFFRACTION1allA201
4X-RAY DIFFRACTION1allA301 - 435
5X-RAY DIFFRACTION1allB - A201 - 346

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