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- PDB-6qe4: Re-refinement of 5OLI human IBA57-I3C -

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Basic information

Entry
Database: PDB / ID: 6qe4
TitleRe-refinement of 5OLI human IBA57-I3C
ComponentsPutative transferase CAF17, mitochondrial
KeywordsPROTEIN BINDING / Mitochondrial protein / Fe-S protein biogenesis / infantile leukodystrophy / I3C phasing.
Function / homology
Function and homology information


heme biosynthetic process / iron-sulfur cluster assembly / mitochondrial matrix / mitochondrion / RNA binding
Similarity search - Function
: / CAF17, C-terminal beta-barrel domain / YgfZ/GcvT conserved site / YgfZ/GcvT / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1
Similarity search - Domain/homology
Chem-I3C / Iron-sulfur cluster assembly factor IBA57, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.3 Å
AuthorsCalderone, V. / Ciofi-Baffoni, S. / Gourdoupis, S. / Banci, L. / Nasta, V.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity.
Authors: Gourdoupis, S. / Nasta, V. / Ciofi-Baffoni, S. / Banci, L. / Calderone, V.
History
DepositionJan 4, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionMar 13, 2019ID: 5OLI
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transferase CAF17, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2025
Polymers34,9671
Non-polymers2,2354
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.111, 43.048, 59.281
Angle α, β, γ (deg.)77.92, 75.63, 71.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative transferase CAF17, mitochondrial / Iron-sulfur cluster assembly factor homolog


Mass: 34967.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE ELECTRON DENSITY QUALITY IN THE FOLLOWING LOOP REGIONS OF CHAIN A IS VERY POOR OR ABSENT: 53-59, 88-93, 116-117, 137-146, 150-151, 297-300, 306-311.
Source: (gene. exp.) Homo sapiens (human) / Gene: IBA57, C1orf69 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T440, EC: 2.1.-.-
#2: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 20% PEG 6000, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jul 12, 2017 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→56.84 Å / Num. obs: 14998 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 39.36 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / Net I/σ(I): 6.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.87 / % possible all: 97.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
BUSTER2.10.3refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→56.84 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.862 / SU R Cruickshank DPI: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.314 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.23
RfactorNum. reflection% reflectionSelection details
Rfree0.228 800 5.25 %RANDOM
Rwork0.206 ---
obs0.208 15231 100 %-
Displacement parametersBiso mean: 45.89 Å2
Baniso -1Baniso -2Baniso -3
1--7.6876 Å21.9728 Å2-6.7954 Å2
2--7.0027 Å21.4189 Å2
3---0.6849 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.3→56.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 64 76 2483
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012470HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073377HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d802SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes461HARMONIC5
X-RAY DIFFRACTIONt_it2470HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion18.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion298SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2715SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.2662 -4.99 %
Rwork0.2271 362 -
all0.2291 381 -
obs--99.48 %
Refinement TLS params.Method: refined / Origin x: 32.2415 Å / Origin y: 42.6241 Å / Origin z: 37.2518 Å
111213212223313233
T-0.1936 Å20.0098 Å2-0.0053 Å2--0.0944 Å20.0239 Å2--0.0044 Å2
L2.1348 °20.4982 °2-0.0618 °2-4.5474 °20.2388 °2--3.6761 °2
S0.0379 Å °0.0438 Å °0.0376 Å °-0.047 Å °0.0303 Å °0.1153 Å °-0.1012 Å °-0.0121 Å °-0.0682 Å °
Refinement TLS groupSelection details: { A|17 - A|324 }

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