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- PDB-6pi6: The evolving story of AtzT, a periplasmic binding protein -

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Basic information

Entry
Database: PDB / ID: 6pi6
TitleThe evolving story of AtzT, a periplasmic binding protein
ComponentsAtrazine periplasmic binding protein
KeywordsTRANSPORT PROTEIN / SAD phasing / periplasmic binding protein / evolution from purine binding to atrazine binding
Function / homology
Function and homology information


metal ion binding / plasma membrane
Similarity search - Function
ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-OKM / ABC transporter substrate-binding protein PnrA-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPeat, T.S. / Newman, J. / Scott, C. / Esquirol, L. / Dennis, M. / Nebl, T.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: The evolving story of AtzT, a periplasmic binding protein.
Authors: Dennis, M.L. / Esquirol, L. / Nebl, T. / Newman, J. / Scott, C. / Peat, T.S.
History
DepositionJun 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atrazine periplasmic binding protein
B: Atrazine periplasmic binding protein
C: Atrazine periplasmic binding protein
D: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,0349
Polymers153,1674
Non-polymers8675
Water14,376798
1
A: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5673
Polymers38,2921
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4892
Polymers38,2921
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4892
Polymers38,2921
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4892
Polymers38,2921
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.761, 62.786, 120.173
Angle α, β, γ (deg.)90.000, 93.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA28 - 36023 - 355
21LYSLYSBB28 - 36023 - 355
12THRTHRAA28 - 35723 - 352
22THRTHRCC28 - 35723 - 352
13THRTHRAA28 - 35723 - 352
23THRTHRDD28 - 35723 - 352
14THRTHRBB28 - 35723 - 352
24THRTHRCC28 - 35723 - 352
15THRTHRBB28 - 35723 - 352
25THRTHRDD28 - 35723 - 352
16ILEILECC28 - 35823 - 353
26ILEILEDD28 - 35823 - 353

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Atrazine periplasmic binding protein


Mass: 38291.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (strain ADP) (bacteria)
Strain: ADP / Gene: orf97, AOX63_31690 / Production host: Escherichia coli (E. coli) / References: UniProt: Q936X6
#2: Chemical
ChemComp-OKM / 4-(ethylamino)-6-[(propan-2-yl)amino]-1,3,5-triazin-2-ol


Mass: 197.238 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 20 mg/mL in SD2 plates incubated at 20 C. Crystallisation conditions contained 6-8% Jeffamine M600 with 2-7% MPD and trisodium citrate at 1.1-1.2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953716 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953716 Å / Relative weight: 1
ReflectionResolution: 1.65→49.1 Å / Num. obs: 176707 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Net I/σ(I): 10.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 7 % / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8668 / CC1/2: 0.653 / Rpim(I) all: 0.515 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PII

6pii


Resolution: 1.65→49.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.984 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.079
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1818 8885 5 %RANDOM
Rwork0.162 ---
obs0.163 167790 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.06 Å2 / Biso mean: 27.596 Å2 / Biso min: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0 Å2-0.24 Å2
2--2.11 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.65→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10048 0 60 798 10906
Biso mean--26.8 36.91 -
Num. residues----1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01310591
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179950
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.64814391
X-RAY DIFFRACTIONr_angle_other_deg1.4621.58523159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94751376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01924.077439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.836151763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7551529
X-RAY DIFFRACTIONr_chiral_restr0.0850.21362
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022099
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110690.05
12B110690.05
21A108480.07
22C108480.07
31A108430.07
32D108430.07
41B107520.06
42C107520.06
51B107630.06
52D107630.06
61C108960.05
62D108960.05
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 672 -
Rwork0.281 12348 -
all-13020 -
obs--99.97 %

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