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

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Basic information

Entry
Database: PDB / ID: 6pii
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
ETHYL MERCURY ION / GUANINE / PHOSPHATE ION / ABC transporter substrate-binding protein PnrA-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 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 1.2Mar 13, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
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 / _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)154,92015
Polymers153,1674
Non-polymers1,75311
Water11,674648
1
A: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7674
Polymers38,2921
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7674
Polymers38,2921
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7134
Polymers38,2921
Non-polymers4213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Atrazine periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6723
Polymers38,2921
Non-polymers3812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.920, 63.050, 120.436
Angle α, β, γ (deg.)90.00, 93.49, 90.00
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPROPROAA27 - 35922 - 354
21GLNGLNPROPROBB27 - 35922 - 354
12GLUGLUTHRTHRAA28 - 35723 - 352
22GLUGLUTHRTHRCC28 - 35723 - 352
13GLUGLUTHRTHRAA28 - 35723 - 352
23GLUGLUTHRTHRDD28 - 35723 - 352
14GLUGLUTHRTHRBB28 - 35723 - 352
24GLUGLUTHRTHRCC28 - 35723 - 352
15GLUGLUTHRTHRBB28 - 35723 - 352
25GLUGLUTHRTHRDD28 - 35723 - 352
16GLUGLUILEILECC28 - 35823 - 353
26GLUGLUILEILEDD28 - 35823 - 353

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 659 molecules

#2: Chemical
ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5Hg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 20 mg/mL in SD2 plates incubated at 20 C. 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: 1.00802 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00802 Å / Relative weight: 1
ReflectionResolution: 1.87→49.4 Å / Num. obs: 119947 / % possible obs: 97.8 % / Redundancy: 19.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.032 / Net I/σ(I): 13.5
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4833 / CC1/2: 0.809 / Rpim(I) all: 0.246 / % possible all: 80.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
ADDREFdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→49.4 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.469 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18303 5791 4.8 %RANDOM
Rwork0.15486 ---
obs0.15624 114140 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.759 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å2-0 Å22.47 Å2
2---2 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.87→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10065 0 67 648 10780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01310464
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179771
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.64114202
X-RAY DIFFRACTIONr_angle_other_deg1.4121.57922724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82251348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01824.009434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.805151722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2291529
X-RAY DIFFRACTIONr_chiral_restr0.0770.21349
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022071
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8723.1835374
X-RAY DIFFRACTIONr_mcbond_other2.8713.1835373
X-RAY DIFFRACTIONr_mcangle_it3.6984.7546728
X-RAY DIFFRACTIONr_mcangle_other3.6974.7556729
X-RAY DIFFRACTIONr_scbond_it4.4353.6375090
X-RAY DIFFRACTIONr_scbond_other4.4053.6345082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5995.2177463
X-RAY DIFFRACTIONr_long_range_B_refined7.08961.14845465
X-RAY DIFFRACTIONr_long_range_B_other7.07661.06445053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A108350.05
12B108350.05
21A105650.08
22C105650.08
31A105750.07
32D105750.07
41B105850.08
42C105850.08
51B105950.08
52D105950.08
61C106360.06
62D106360.06
LS refinement shellResolution: 1.869→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 374 -
Rwork0.228 7356 -
obs--85.65 %

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