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- PDB-4zpj: ABC transporter substrate-binding protein from Sphaerobacter ther... -

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Basic information

Entry
Database: PDB / ID: 4zpj
TitleABC transporter substrate-binding protein from Sphaerobacter thermophilus
ComponentsExtracellular ligand-binding receptor
KeywordsTRANSPORT PROTEIN / ABC transporter / substrate-binding protein / DUF3597 / structural genomics / APC111067 / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homology
Function and homology information


Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsOSIPIUK, J. / Holowicki, J. / Clancy, S. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: to be published
Title: ABC transporter substrate-binding protein from Sphaerobacter thermophilus.
Authors: OSIPIUK, J. / Holowicki, J. / Clancy, S. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,96022
Polymers44,8261
Non-polymers1,13421
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.818, 88.531, 99.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Extracellular ligand-binding receptor


Mass: 44825.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (strain DSM 20745 / S 6022) (bacteria)
Strain: DSM 20745 / S 6022 / Gene: Sthe_0207 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D1C6A8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M zinc acetate, 0.1 M imidazole-HCl buffer, 20% 1,4-butanediol

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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: Feb 23, 2013
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: 2.24→50 Å / Num. all: 20481 / Num. obs: 20481 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Χ2: 1.583 / Net I/av σ(I): 22.631 / Net I/σ(I): 9.8 / Num. measured all: 138486
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.24-2.2850.7632.19970.6980.3710.8510.87299.9
2.28-2.325.70.62510030.8120.2840.6880.899100
2.32-2.366.40.6159910.8850.2620.670.915100
2.36-2.417.10.57310050.8640.2290.6180.931100
2.41-2.477.10.5210280.890.2080.5610.988100
2.47-2.527.20.4359860.9350.1730.4691.014100
2.52-2.597.20.36510150.9540.1450.3931.031100
2.59-2.667.20.31710090.9610.1260.3421.061100
2.66-2.737.20.27710040.9660.110.2981.236100
2.73-2.827.20.23210120.9750.0920.251.343100
2.82-2.927.20.20210330.9820.080.2181.477100
2.92-3.047.20.1739970.9870.0690.1871.548100
3.04-3.187.10.14410180.9910.0580.1561.766100
3.18-3.357.10.1210290.9930.0480.131.894100
3.35-3.567.10.10110220.9930.040.1081.96100
3.56-3.836.90.08510350.9960.0350.0921.972100
3.83-4.226.70.08110440.9950.0340.0882.139100
4.22-4.826.50.07710390.9960.0320.0842.346100
4.82-6.086.40.07810690.9960.0330.0852.637100
6.08-5060.06811450.9960.0290.0743.47199.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→43.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.275 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1048 5.1 %RANDOM
Rwork0.1712 ---
obs0.1737 19381 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.09 Å2 / Biso mean: 46.889 Å2 / Biso min: 28.97 Å2
Baniso -1Baniso -2Baniso -3
1--4.19 Å2-0 Å20 Å2
2---0.05 Å20 Å2
3---4.24 Å2
Refinement stepCycle: final / Resolution: 2.24→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 21 72 2917
Biso mean--67.88 47.68 -
Num. residues----371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192896
X-RAY DIFFRACTIONr_bond_other_d0.0010.022728
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9763946
X-RAY DIFFRACTIONr_angle_other_deg0.87936263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14424.468141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48515431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8271521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
X-RAY DIFFRACTIONr_mcbond_it2.0992.7321489
X-RAY DIFFRACTIONr_mcbond_other2.0922.7311488
X-RAY DIFFRACTIONr_mcangle_it2.9354.0921861
LS refinement shellResolution: 2.243→2.301 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 80 -
Rwork0.247 1358 -
all-1438 -
obs--98.29 %
Refinement TLS params.Method: refined / Origin x: 36.6471 Å / Origin y: 61.9565 Å / Origin z: 33.7909 Å
111213212223313233
T0.2109 Å20.0511 Å20.0205 Å2-0.1556 Å20.0052 Å2--0.0028 Å2
L1.33 °20.2575 °2-0.2591 °2-1.2792 °20.33 °2--0.9648 °2
S0.0755 Å °0.202 Å °0.001 Å °-0.1101 Å °-0.097 Å °-0.0259 Å °0.0321 Å °-0.106 Å °0.0215 Å °

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