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- PDB-4lr3: Crystal structure of E. coli YfbU at 2.5 A resolution -

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Basic information

Entry
Database: PDB / ID: 4lr3
TitleCrystal structure of E. coli YfbU at 2.5 A resolution
Componentsprotein YfbU
KeywordsAPOPTOSIS / Helical Tetramer
Function / homology
Function and homology information


Helix hairpin bin / yfbu gene product, domain 2 / yfbu gene product, domain 2 / Uncharacterised protein family UPF0304, YfbU / YfbU, helix-hairpin domain superfamily / YfbU, alpha-helical bundle domain superfamily / YfbU domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / UPF0304 protein YfbU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD/SIR / Resolution: 2.5 Å
AuthorsWang, J. / Wing, R.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data.
Authors: Wang, J. / Wing, R.A.
#1: Journal: To be Published
Title: Single-atom approximation and refinement of heavy-atom cluster derivatives
Authors: Wang, J. / Wing, R.A.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: protein YfbU
B: protein YfbU
C: protein YfbU
D: protein YfbU
E: protein YfbU
F: protein YfbU
G: protein YfbU
H: protein YfbU
I: protein YfbU
J: protein YfbU
K: protein YfbU
L: protein YfbU
M: protein YfbU
N: protein YfbU
O: protein YfbU
P: protein YfbU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,92671
Polymers312,96316
Non-polymers2,96255
Water24,0501335
1
A: protein YfbU
B: protein YfbU
C: protein YfbU
D: protein YfbU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00518
Polymers78,2414
Non-polymers76414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-125 kcal/mol
Surface area33700 Å2
MethodPISA
2
E: protein YfbU
F: protein YfbU
G: protein YfbU
H: protein YfbU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,91017
Polymers78,2414
Non-polymers66913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-125 kcal/mol
Surface area33700 Å2
MethodPISA
3
I: protein YfbU
J: protein YfbU
K: protein YfbU
L: protein YfbU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00518
Polymers78,2414
Non-polymers76414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-124 kcal/mol
Surface area33730 Å2
MethodPISA
4
M: protein YfbU
N: protein YfbU
O: protein YfbU
P: protein YfbU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00518
Polymers78,2414
Non-polymers76414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-126 kcal/mol
Surface area33830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.078, 230.078, 230.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11N-323-

HOH

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Components

#1: Protein
protein YfbU


Mass: 19560.213 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: E2QPF5
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1335 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6 M ammonium phosphate monobasic, 100 mM MES, pH 5.5 or 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.2146
SYNCHROTRONAPS 24-ID-C21.0086
SYNCHROTRONNSLS X29A30.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 28, 2013
DECTRIS PILATUS 6M2PIXELFeb 22, 2013
ADSC QUANTUM 315r3CCDMar 28, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double crystal sagittal focusing Si(111)SINGLE WAVELENGTHMx-ray1
2Cryo-Cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
3Rosenbaum-Rock double crystal sagittal focusing Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.21461
21.00861
30.9791
ReflectionResolution: 2.5→56 Å / Num. all: 139809 / Num. obs: 138551 / % possible obs: 99.1 %
Reflection shellHighest resolution: 2.5 Å

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
MLPHAREphasing
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD/SIR / Resolution: 2.5→55.8 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 30.255 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24703 6945 5 %RANDOM
Rwork0.20789 ---
obs0.20986 131307 99.14 %-
all-139809 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.572 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21904 0 147 1335 23386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01922661
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220828
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.94730791
X-RAY DIFFRACTIONr_angle_other_deg1.125347403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.81852610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06923.3231297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.296154003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.07115241
X-RAY DIFFRACTIONr_chiral_restr0.0610.23121
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0225820
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025925
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3754.19310482
X-RAY DIFFRACTIONr_mcbond_other2.3754.19310481
X-RAY DIFFRACTIONr_mcangle_it2.846.28913075
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1674.84912179
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.673343489
X-RAY DIFFRACTIONr_sphericity_free22.9215480
X-RAY DIFFRACTIONr_sphericity_bonded7.641543743
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 498 -
Rwork0.397 9061 -
obs--93.52 %

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