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

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Basic information

Entry
Database: PDB / ID: 6bju
TitleThe structure of AtzH: a little known member of the atrazine breakdown pathway
ComponentsAtzH
KeywordsUNKNOWN FUNCTION / Atrazine ancillary protein
Function / homologyAtzH-like / AtzH-like / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF4440 domain-containing protein
Function and homology information
Biological speciesPseudomonas sp. EGD-AKN5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.64 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 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: AtzH
B: AtzH
C: AtzH
D: AtzH


Theoretical massNumber of molelcules
Total (without water)69,9704
Polymers69,9704
Non-polymers00
Water9,170509
1
A: AtzH
B: AtzH


Theoretical massNumber of molelcules
Total (without water)34,9852
Polymers34,9852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-17 kcal/mol
Surface area11060 Å2
MethodPISA
2
C: AtzH
D: AtzH


Theoretical massNumber of molelcules
Total (without water)34,9852
Polymers34,9852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-17 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.809, 51.831, 59.679
Angle α, β, γ (deg.)99.81, 102.15, 92.48
Int Tables number1
Space group name H-MP1
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
11METMETALAALAAA1 - 12823 - 150
21METMETALAALABB1 - 12823 - 150
12LEULEULEULEUAA2 - 12924 - 151
22LEULEULEULEUCC2 - 12924 - 151
13METMETLEULEUAA1 - 12923 - 151
23METMETLEULEUDD1 - 12923 - 151
14LEULEUALAALABB2 - 12824 - 150
24LEULEUALAALACC2 - 12824 - 150
15METMETALAALABB1 - 12823 - 150
25METMETALAALADD1 - 12823 - 150
16LEULEULEULEUCC2 - 12924 - 151
26LEULEULEULEUDD2 - 12924 - 151

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
AtzH / DUF4440 domain-containing protein


Mass: 17492.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. EGD-AKN5 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1A5DB13
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein was at 4 mg/mL and set up in equal volume with the reservoir (150 nL plus 150 nL) with the reservoir conditions being: 20% (w/v) PEG 6000, 2.5% tert-butanol (v/v) and 100 mM sodium ...Details: Protein was at 4 mg/mL and set up in equal volume with the reservoir (150 nL plus 150 nL) with the reservoir conditions being: 20% (w/v) PEG 6000, 2.5% tert-butanol (v/v) and 100 mM sodium citrate buffer at pH 5.5

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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: 1.64→50.4 Å / Num. obs: 71033 / % possible obs: 97.2 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Net I/σ(I): 7.8
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3498 / CC1/2: 0.733 / Rpim(I) all: 0.581 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.64→50.4 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.046 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22812 3265 4.6 %RANDOM
Rwork0.19901 ---
obs0.20033 67428 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.627 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.85 Å20 Å2
2---0.24 Å2-0.12 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.64→50.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 0 509 4411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194119
X-RAY DIFFRACTIONr_bond_other_d0.0030.023694
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9175620
X-RAY DIFFRACTIONr_angle_other_deg1.04238478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5823.069202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35115654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4231538
X-RAY DIFFRACTIONr_chiral_restr0.1220.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02936
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_it2.3771.9972046
X-RAY DIFFRACTIONr_mcbond_other2.3771.9952045
X-RAY DIFFRACTIONr_mcangle_it3.6852.952568
X-RAY DIFFRACTIONr_mcangle_other3.6842.9522569
X-RAY DIFFRACTIONr_scbond_it3.0032.2252073
X-RAY DIFFRACTIONr_scbond_other3.0032.2272074
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5233.2213053
X-RAY DIFFRACTIONr_long_range_B_refined7.10136.61417176
X-RAY DIFFRACTIONr_long_range_B_other6.99835.88816634
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)
11A78640.08
12B78640.08
21A82000.06
22C82000.06
31A78040.1
32D78040.1
41B76760.08
42C76760.08
51B77880.07
52D77880.07
61C75920.09
62D75920.09
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 221 -
Rwork0.259 4858 -
obs--94.11 %

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