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- PDB-3r3r: Structure of the YrdA ferripyochelin binding protein from Salmone... -

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Basic information

Entry
Database: PDB / ID: 3r3r
TitleStructure of the YrdA ferripyochelin binding protein from Salmonella enterica
Componentsferripyochelin binding protein
KeywordsTRANSFERASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / all beta protein / single-stranded left-handed beta-helix
Function / homologyHexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta / metal ion binding / Putative ferripyochelin binding protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Structure of the YrdA ferripyochelin binding protein from Salmonella enterica
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_ref_seq_dif / 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_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.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_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_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_ref_seq_dif.details / _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: ferripyochelin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3572
Polymers20,2921
Non-polymers651
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ferripyochelin binding protein
hetero molecules

A: ferripyochelin binding protein
hetero molecules

A: ferripyochelin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0726
Polymers60,8763
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6930 Å2
ΔGint-144 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.43, 99.43, 46.66
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-388-

HOH

21A-409-

HOH

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Components

#1: Protein ferripyochelin binding protein


Mass: 20292.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: yrdA, STM3399 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8ZLN3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 700 mM sodium citrate, 10 mM magnesium chloride, 50 mM HEPES, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2010 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 53953 / Num. obs: 53413 / % possible obs: 99 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 2.8 / Redundancy: 17.4 % / Biso Wilson estimate: 13.43 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 36.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique all% possible all
1.2-1.247.50.5832.8499192.1
1.24-1.2911.50.4685.2532298.5
1.29-1.35160.3978.75359100
1.35-1.4218.90.30711.95419100
1.42-1.5119.80.20417.75374100
1.51-1.63200.134255380100
1.63-1.7920.10.10928.35405100
1.79-2.0520.10.09529.55386100
2.05-2.5920.10.07734.15406100
2.59-5019.50.0646.8537199.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→31.64 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.14 / σ(F): 1.44 / σ(I): 2.8 / Phase error: 14.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.16 2670 5 %RANDOM
Rwork0.138 ---
obs0.139 53379 99 %-
all-53935 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.488 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 83.3 Å2 / Biso mean: 19.97 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0 Å2
2---0.58 Å20 Å2
3---4.04 Å2
Refinement stepCycle: LAST / Resolution: 1.2→31.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 1 366 1762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091510
X-RAY DIFFRACTIONf_angle_d1.342072
X-RAY DIFFRACTIONf_chiral_restr0.091237
X-RAY DIFFRACTIONf_plane_restr0.008270
X-RAY DIFFRACTIONf_dihedral_angle_d11.165576
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.2-1.240.30922480.288547394987498791.9
1.24-1.290.25332620.220550595321532198.4
1.29-1.350.19692660.1665510853745374100
1.35-1.420.17032690.1364513154005400100
1.42-1.510.1472670.1159510653735373100
1.51-1.630.14362710.1055509853695369100
1.63-1.790.14912710.1165513654075407100
1.79-2.050.13822680.127851195387538799.9
2.05-2.580.16112730.1357513254055405100
2.58-31.650.15162750.136250815356535699.6

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