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- PDB-3ry3: Putative solute-binding protein from Yersinia pestis. -

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Basic information

Entry
Database: PDB / ID: 3ry3
TitlePutative solute-binding protein from Yersinia pestis.
ComponentsPutative solute-binding protein
KeywordsTRANSPORT PROTEIN / structural genomics / IDP00509 / Center for Structural Genomics of Infectious Diseases / CSGID / solute-binding
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ABC transporter substrate-binding protein / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.43 Å
AuthorsOsipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Putative solute-binding protein from Yersinia pestis.
Authors: Osipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative solute-binding protein
B: Putative solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4484
Polymers117,3302
Non-polymers1182
Water3,603200
1
A: Putative solute-binding protein


Theoretical massNumber of molelcules
Total (without water)58,6651
Polymers58,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7833
Polymers58,6651
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.036, 171.322, 128.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative solute-binding protein / Putative substrate-binding periplasmic protein of ABC transporter


Mass: 58665.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: oppA4, y1231, YPO2660, YP_2461 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7CJS8, UniProt: A0A2U2H355*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.69 Å3/Da / Density % sol: 66.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8 M sodium acetate trihydrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.43→43.1 Å / Num. all: 64629 / Num. obs: 64629 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.121 / Χ2: 2.122 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.43-2.516.80.8042.3231851.19799.9
2.51-2.567.10.79432021.31100
2.56-2.617.20.72331811.253100
2.61-2.667.30.62832101.306100
2.66-2.727.40.56932071.327100
2.72-2.787.40.46631891.249100
2.78-2.857.50.40131911.362100
2.85-2.937.50.32832351.24100
2.93-3.017.50.28632101.221100
3.01-3.117.50.24132041.255100
3.11-3.227.50.1931991.3100
3.22-3.357.50.14832281.456100
3.35-3.57.50.12232301.584100
3.5-3.697.40.09632341.82100
3.69-3.927.40.08332322.133100
3.92-4.227.40.07932362.698100
4.22-4.657.30.07432663.327100
4.65-5.327.10.08132684.345100
5.32-6.770.08632934.756100
6.7-506.90.06534296.42499.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.43→43.1 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 13.171 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3265 5.1 %RANDOM
Rwork0.1728 ---
all0.1745 64459 --
obs0.1745 64459 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.34 Å2 / Biso mean: 43.9043 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---2.01 Å20 Å2
3---2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.43→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7617 0 8 200 7825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.020.0227902
X-RAY DIFFRACTIONf_bond_other_d0.0010.025232
X-RAY DIFFRACTIONf_angle_refined_deg1.6341.94210782
X-RAY DIFFRACTIONf_angle_other_deg0.93312799
X-RAY DIFFRACTIONf_dihedral_angle_1_deg6.2085993
X-RAY DIFFRACTIONf_dihedral_angle_2_deg39.56825.054368
X-RAY DIFFRACTIONf_dihedral_angle_3_deg17.145151245
X-RAY DIFFRACTIONf_dihedral_angle_4_deg21.9441531
X-RAY DIFFRACTIONf_chiral_restr0.0950.21150
X-RAY DIFFRACTIONf_gen_planes_refined0.0080.0218937
X-RAY DIFFRACTIONf_gen_planes_other0.0010.021546
X-RAY DIFFRACTIONf_mcbond_it0.9831.54901
X-RAY DIFFRACTIONf_mcbond_other0.1791.51992
X-RAY DIFFRACTIONf_mcangle_it1.92927866
X-RAY DIFFRACTIONf_scbond_it2.92533001
X-RAY DIFFRACTIONf_scangle_it4.7344.52908
LS refinement shellResolution: 2.43→2.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 173 -
Rwork0.266 3383 -
all-3556 -
obs-3556 73.99 %
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)
10.90080.36140.32130.55360.08610.1310.00410.04730.0924-0.1183-0.0287-0.10610.00620.0170.02460.07280.00340.04010.04210.02130.117428.220917.346520.4858
21.28810.7277-0.24650.5356-0.15850.05150.02650.0284-0.155-0.0608-0.0478-0.0298-0.00130.01220.02140.1108-0.0091-0.02860.0821-0.01150.103850.739765.866818.6176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 521
2X-RAY DIFFRACTION1A526 - 628
3X-RAY DIFFRACTION2B30 - 521
4X-RAY DIFFRACTION2B701 - 702
5X-RAY DIFFRACTION2B526 - 622

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