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- PDB-6bjt: The structure of AtzH: a little known member of the atrazine brea... -

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Basic information

Entry
Database: PDB / ID: 6bjt
TitleThe structure of AtzH: a little known member of the atrazine breakdown pathway
ComponentsDUF4440 domain-containing protein
KeywordsUNKNOWN FUNCTION / Atrazine ancillary protein
Function / homology
Function and homology information


AtzH-like / AtzH-like / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DI(HYDROXYETHYL)ETHER / DUF4440 domain-containing protein
Similarity search - Component
Biological speciesPseudomonas sp. EGD-AKN5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPeat, T.S. / Newman, J. / Scott, C. / Esquirol, L.
CitationJournal: PLoS ONE / Year: 2018
Title: A novel decarboxylating amidohydrolase involved in avoiding metabolic dead ends during cyanuric acid catabolism in Pseudomonas sp. strain ADP.
Authors: Esquirol, L. / Peat, T.S. / Wilding, M. / Hartley, C.J. / Newman, J. / Scott, C.
History
DepositionNov 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: DUF4440 domain-containing protein
B: DUF4440 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2736
Polymers34,9852
Non-polymers2884
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-12 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.465, 74.977, 96.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-395-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 129 / Label seq-ID: 25 - 151

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein DUF4440 domain-containing protein


Mass: 17492.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. EGD-AKN5 (bacteria) / Gene: BAE52_00115 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1A5DB13
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.84 Å3/Da / Density % sol: 33.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein was concentrated to 4 mg/mL and set up with and equal volume of reservoir (150 nL plus 150 nL) with the reservoir contents being: 200 mM ammonium acetate, 30% PEG 4000, 100 mM ...Details: The protein was concentrated to 4 mg/mL and set up with and equal volume of reservoir (150 nL plus 150 nL) with the reservoir contents being: 200 mM ammonium acetate, 30% PEG 4000, 100 mM sodium acetate buffer at pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.8→51.73 Å / Num. obs: 24359 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.063 / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.549 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1442 / CC1/2: 0.837 / Rpim(I) all: 0.622 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rcd

2rcd


Resolution: 1.8→51.73 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.774 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20645 1197 4.9 %RANDOM
Rwork0.16247 ---
obs0.16459 23104 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.236 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å2-0 Å2-0 Å2
2---0.38 Å20 Å2
3---2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.8→51.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 19 178 2239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192177
X-RAY DIFFRACTIONr_bond_other_d0.0020.021969
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9252969
X-RAY DIFFRACTIONr_angle_other_deg1.02534516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15122.43107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94815338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6531524
X-RAY DIFFRACTIONr_chiral_restr0.1030.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
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_it2.7282.4931071
X-RAY DIFFRACTIONr_mcbond_other2.6982.4871068
X-RAY DIFFRACTIONr_mcangle_it4.3913.7061345
X-RAY DIFFRACTIONr_mcangle_other4.3913.711346
X-RAY DIFFRACTIONr_scbond_it2.9812.7561106
X-RAY DIFFRACTIONr_scbond_other2.9812.7561106
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5534.0181625
X-RAY DIFFRACTIONr_long_range_B_refined7.98545.0938932
X-RAY DIFFRACTIONr_long_range_B_other7.98545.0958933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7946 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 99 -
Rwork0.23 1696 -
obs--99.45 %

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