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- PDB-6b2x: Apo YiuA Crystal Form 1 -

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Basic information

Entry
Database: PDB / ID: 6b2x
TitleApo YiuA Crystal Form 1
ComponentsSolute-binding periplasmic protein of iron/siderophore ABC transporter
KeywordsMETAL TRANSPORT / Transition metal homeostasis / Yersinia pestis / Cluster A-2 / Substrate-binding protein
Function / homology: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Solute-binding periplasmic protein of iron/siderophore ABC transporter
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 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
Revision 1.1Oct 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)87,4906
Polymers87,3732
Non-polymers1174
Water7,350408
1
A: Solute-binding periplasmic protein of iron/siderophore ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7453
Polymers43,6871
Non-polymers582
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)43,7453
Polymers43,6871
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.515, 94.732, 171.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.72 % / Description: long thin bars
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-B / Wavelength: 1.2828 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. obs: 34143 / % possible obs: 98.6 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.036 / Net I/σ(I): 15.3
Reflection shellResolution: 2.199→2.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.248 / Num. unique obs: 1605 / CC1/2: 0.984 / Rpim(I) all: 0.162 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000v715data reduction
HKL-2000v715data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MO9

4mo9


Resolution: 2.199→41.465 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.75
RfactorNum. reflection% reflection
Rfree0.2457 1999 5.87 %
Rwork0.1961 --
obs0.199 34079 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.199→41.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 0 4 408 5550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085258
X-RAY DIFFRACTIONf_angle_d0.9927134
X-RAY DIFFRACTIONf_dihedral_angle_d4.3133775
X-RAY DIFFRACTIONf_chiral_restr0.057797
X-RAY DIFFRACTIONf_plane_restr0.008926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1994-2.25440.31041350.23562181X-RAY DIFFRACTION95
2.2544-2.31530.32441370.23442209X-RAY DIFFRACTION99
2.3153-2.38340.27451460.2272323X-RAY DIFFRACTION99
2.3834-2.46030.2711380.22472238X-RAY DIFFRACTION99
2.4603-2.54830.31671430.2272281X-RAY DIFFRACTION99
2.5483-2.65030.35531410.2372265X-RAY DIFFRACTION98
2.6503-2.77090.29151420.22432266X-RAY DIFFRACTION99
2.7709-2.91690.28591430.2272313X-RAY DIFFRACTION99
2.9169-3.09960.26211430.2162287X-RAY DIFFRACTION99
3.0996-3.33890.23131430.20972286X-RAY DIFFRACTION99
3.3389-3.67470.24551460.1922346X-RAY DIFFRACTION100
3.6747-4.2060.22431430.16772299X-RAY DIFFRACTION99
4.206-5.29730.18831470.15852364X-RAY DIFFRACTION99
5.2973-41.47220.21861520.18082422X-RAY DIFFRACTION96

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