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- PDB-6qe3: Re-refinement of 6ESR human IBA57 at 1.75 A resolution -

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Basic information

Entry
Database: PDB / ID: 6qe3
TitleRe-refinement of 6ESR human IBA57 at 1.75 A resolution
ComponentsPutative transferase CAF17, mitochondrial
KeywordsPROTEIN BINDING / Mitochondrial protein / Fe-S protein biogenesis / infantile leukodystrophy
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups / iron-sulfur cluster assembly / heme biosynthetic process / transferase activity / mitochondrial matrix / mitochondrion / RNA binding
Similarity search - Function
YgfZ/GcvT conserved site / YgfZ/GcvT / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1
Similarity search - Domain/homology
Putative transferase CAF17, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCalderone, V. / Ciofi-Baffoni, S. / Gourdoupis, S. / Banci, L.
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: 6ESR
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 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transferase CAF17, mitochondrial


Theoretical massNumber of molelcules
Total (without water)33,2821
Polymers33,2821
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.280, 43.250, 55.300
Angle α, β, γ (deg.)94.88, 93.25, 108.18
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: 33282.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IBA57, C1orf69 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5T440, Transferases; Transferring one-carbon groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationMonochromator: Standard ESRF channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 31785 / % possible obs: 96.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4346 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(dev_3366: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OLI

5oli
PDB Unreleased entry


Resolution: 1.75→40.849 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.32
RfactorNum. reflection% reflection
Rfree0.1971 1589 5 %
Rwork0.1746 --
obs0.1758 31761 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→40.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 0 129 2477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112411
X-RAY DIFFRACTIONf_angle_d1.1453288
X-RAY DIFFRACTIONf_dihedral_angle_d16.3161429
X-RAY DIFFRACTIONf_chiral_restr0.061362
X-RAY DIFFRACTIONf_plane_restr0.009431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7499-1.80640.27251440.25252725X-RAY DIFFRACTION96
1.8064-1.87090.26021410.22972678X-RAY DIFFRACTION94
1.8709-1.94580.23871410.21072677X-RAY DIFFRACTION95
1.9458-2.03440.22491440.19632738X-RAY DIFFRACTION96
2.0344-2.14160.21281440.17712748X-RAY DIFFRACTION97
2.1416-2.27580.23131450.17222744X-RAY DIFFRACTION96
2.2758-2.45150.18161440.17192745X-RAY DIFFRACTION98
2.4515-2.69820.2041470.17092791X-RAY DIFFRACTION98
2.6982-3.08850.20541470.17732796X-RAY DIFFRACTION98
3.0885-3.89070.18511450.16892757X-RAY DIFFRACTION98
3.8907-40.86030.17461470.16092773X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52640.0245-0.06220.5433-0.33171.43380.0449-0.0923-0.0660.1781-0.0181-0.0307-0.00240.12690.00010.2286-0.00140.01020.22080.0010.20521.2326-2.00818.6086
20.1296-0.1637-0.06550.6195-0.21770.2733-0.0292-0.02190.12870.14150.12960.0839-0.3408-0.14660.00010.28420.05630.03050.2702-0.01970.2327-8.10945.159512.4752
30.5092-0.25420.08440.7926-0.17910.65570.0129-0.14580.1070.2175-0.0654-0.1029-0.410.3009-00.2582-0.0688-0.02130.2872-0.02710.2455.54116.524110.7452
40.55810.1155-0.13471.0302-0.10952.28010.0549-0.0663-0.04780.0041-0.02140.08370.1339-0.064300.1509-0.0053-0.00740.20080.00460.2222-4.1521-5.72242.23
50.2862-0.0413-0.20830.1763-0.3150.86040.11780.20610.072-0.1003-0.07990.0509-0.4464-0.1685-0.02490.38570.04950.00750.20830.03230.2113-2.600410.0062-11.9603
60.3809-0.0827-0.15710.2550.25240.32110.07610.1791-0.1177-0.4445-0.06140.00380.34770.3114-0.00010.40660.06930.03970.35860.01220.25926.7736-4.8022-21.1365
70.14890.06280.02570.0150.08170.44090.0540.14890.0377-0.3598-0.0180.09510.1803-0.045800.29710.0434-0.02540.2575-0.01020.2043-0.5704-3.0808-20.7318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 233 )
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 255 )
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 285 )
7X-RAY DIFFRACTION7chain 'A' and (resid 286 through 323 )

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