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- PDB-6b2y: Apo YiuA Crystal Form 2 -

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Basic information

Entry
Database: PDB / ID: 6b2y
TitleApo YiuA Crystal Form 2
ComponentsSolute-binding periplasmic protein of iron/siderophore ABC transporter
KeywordsMETAL TRANSPORT / Yersinia pestis / transition metal homeostasis / substrate-binding protein / periplasm / iron uptake
Function / homologyABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / periplasmic space / Solute-binding periplasmic protein of iron/siderophore ABC transporter
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsRadka, C.D. / DeLucas, L.J. / Aller, S.G.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal.
Authors: Radka, C.D. / Chen, D. / DeLucas, L.J. / Aller, S.G.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
SupersessionNov 29, 2017ID: 5WFA
Revision 1.1Nov 29, 2017Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute-binding periplasmic protein of iron/siderophore ABC transporter
B: Solute-binding periplasmic protein of iron/siderophore ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4425
Polymers87,3732
Non-polymers693
Water11,151619
1
A: Solute-binding periplasmic protein of iron/siderophore ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7333
Polymers43,6871
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Solute-binding periplasmic protein of iron/siderophore ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7102
Polymers43,6871
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.371, 97.012, 74.284
Angle α, β, γ (deg.)90.00, 100.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Solute-binding periplasmic protein of iron/siderophore ABC transporter


Mass: 43686.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yiuA, y2875 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8D027
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 1.87 Å3/Da / Density % sol: 34.18 % / Description: tetragonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 20% PEG 3350, 10 mM MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.2398 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 57167 / % possible obs: 90.9 % / Redundancy: 5.1 % / CC1/2: 0.972 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.033 / Net I/σ(I): 36.2
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 5 / Num. unique obs: 2821 / CC1/2: 0.976 / Rpim(I) all: 0.152 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000v715data reduction
HKL-2000v715data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WF8

5wf8
PDB Unreleased entry


Resolution: 1.77→45.566 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2187 2000 3.5 %
Rwork0.186 --
obs0.1871 57135 90.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.77→45.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 3 619 5791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075281
X-RAY DIFFRACTIONf_angle_d0.8567168
X-RAY DIFFRACTIONf_dihedral_angle_d5.3913182
X-RAY DIFFRACTIONf_chiral_restr0.057802
X-RAY DIFFRACTIONf_plane_restr0.005931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.81430.26141420.22933923X-RAY DIFFRACTION91
1.8143-1.86330.3071460.22454028X-RAY DIFFRACTION93
1.8633-1.91820.26071460.21784028X-RAY DIFFRACTION94
1.9182-1.98010.22831460.214005X-RAY DIFFRACTION93
1.9801-2.05080.28521440.21563978X-RAY DIFFRACTION92
2.0508-2.1330.26781410.21263894X-RAY DIFFRACTION90
2.133-2.230.25061430.21123927X-RAY DIFFRACTION90
2.23-2.34760.28491330.21033675X-RAY DIFFRACTION85
2.3476-2.49470.22561350.20923721X-RAY DIFFRACTION86
2.4947-2.68730.25051350.21473713X-RAY DIFFRACTION86
2.6873-2.95770.26121360.20793754X-RAY DIFFRACTION87
2.9577-3.38550.19941480.18844072X-RAY DIFFRACTION94
3.3855-4.26490.17821480.16354089X-RAY DIFFRACTION94
4.2649-45.58150.18251570.14864328X-RAY DIFFRACTION98

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