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- PDB-7lkk: Crystal structure of Helicobacter pylori aminofutalosine deaminas... -

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Basic information

Entry
Database: PDB / ID: 7lkk
TitleCrystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) in complex with Methylthio-coformycin
ComponentsAminofutalosine deaminase
KeywordsHYDROLASE/INHIBITOR / Aminofutalosine deaminase / AFLDA / Inhibitor / Inhibitor complex / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homologyhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / : / Chem-MCF / Putative
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHarijan, R.K. / Feng, M. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: Biochemistry / Year: 2021
Title: Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter pylori .
Authors: Feng, M. / Harijan, R.K. / Harris, L.D. / Tyler, P.C. / Frohlich, R.F.G. / Brown, M. / Schramm, V.L.
History
DepositionFeb 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Aminofutalosine deaminase
B: Aminofutalosine deaminase
C: Aminofutalosine deaminase
D: Aminofutalosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,36825
Polymers190,0814
Non-polymers2,28821
Water17,493971
1
A: Aminofutalosine deaminase
B: Aminofutalosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,15312
Polymers95,0402
Non-polymers1,11310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-2 kcal/mol
Surface area30440 Å2
MethodPISA
2
C: Aminofutalosine deaminase
D: Aminofutalosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,21513
Polymers95,0402
Non-polymers1,17511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-4 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.905, 73.072, 157.440
Angle α, β, γ (deg.)90.000, 98.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 4 or resid 6...
21(chain B and (resid 2 through 4 or resid 6...
31(chain C and (resid 2 through 4 or resid 6...
41(chain D and (resid 2 through 4 or resid 6...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNILEILE(chain A and (resid 2 through 4 or resid 6...AA2 - 416 - 18
12GLYGLYPROPRO(chain A and (resid 2 through 4 or resid 6...AA6 - 4520 - 59
13GLNGLNILEILE(chain A and (resid 2 through 4 or resid 6...AA-1 - 40913 - 423
14GLNGLNILEILE(chain A and (resid 2 through 4 or resid 6...AA-1 - 40913 - 423
15GLNGLNILEILE(chain A and (resid 2 through 4 or resid 6...AA-1 - 40913 - 423
16GLNGLNILEILE(chain A and (resid 2 through 4 or resid 6...AA-1 - 40913 - 423
17GLNGLNILEILE(chain A and (resid 2 through 4 or resid 6...AA-1 - 40913 - 423
18GLNGLNILEILE(chain A and (resid 2 through 4 or resid 6...AA-1 - 40913 - 423
21GLNGLNILEILE(chain B and (resid 2 through 4 or resid 6...BB2 - 416 - 18
22GLYGLYLEULEU(chain B and (resid 2 through 4 or resid 6...BB6 - 4720 - 61
23LYSLYSALAALA(chain B and (resid 2 through 4 or resid 6...BB48 - 4962 - 63
24METMETILEILE(chain B and (resid 2 through 4 or resid 6...BB1 - 40915 - 423
25METMETILEILE(chain B and (resid 2 through 4 or resid 6...BB1 - 40915 - 423
26METMETILEILE(chain B and (resid 2 through 4 or resid 6...BB1 - 40915 - 423
27METMETILEILE(chain B and (resid 2 through 4 or resid 6...BB1 - 40915 - 423
31GLNGLNILEILE(chain C and (resid 2 through 4 or resid 6...CC2 - 416 - 18
32GLYGLYPROPRO(chain C and (resid 2 through 4 or resid 6...CC6 - 4520 - 59
33GLNGLNILEILE(chain C and (resid 2 through 4 or resid 6...CC2 - 40916 - 423
34GLNGLNILEILE(chain C and (resid 2 through 4 or resid 6...CC2 - 40916 - 423
35GLNGLNILEILE(chain C and (resid 2 through 4 or resid 6...CC2 - 40916 - 423
36GLNGLNILEILE(chain C and (resid 2 through 4 or resid 6...CC2 - 40916 - 423
37GLNGLNILEILE(chain C and (resid 2 through 4 or resid 6...CC2 - 40916 - 423
38GLNGLNILEILE(chain C and (resid 2 through 4 or resid 6...CC2 - 40916 - 423
41GLNGLNILEILE(chain D and (resid 2 through 4 or resid 6...DD2 - 416 - 18
42GLYGLYPROPRO(chain D and (resid 2 through 4 or resid 6...DD6 - 4520 - 59
43METMETILEILE(chain D and (resid 2 through 4 or resid 6...DD1 - 40915 - 423
44METMETILEILE(chain D and (resid 2 through 4 or resid 6...DD1 - 40915 - 423
45METMETILEILE(chain D and (resid 2 through 4 or resid 6...DD1 - 40915 - 423
46METMETILEILE(chain D and (resid 2 through 4 or resid 6...DD1 - 40915 - 423
47METMETILEILE(chain D and (resid 2 through 4 or resid 6...DD1 - 40915 - 423
48METMETILEILE(chain D and (resid 2 through 4 or resid 6...DD1 - 40915 - 423

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Components

#1: Protein
Aminofutalosine deaminase / AFLDA


Mass: 47520.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: orf1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZMG8
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MCF / (8R)-3-(5-S-methyl-5-thio-beta-D-ribofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol


Mass: 314.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18N4O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.2 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate pH 4.6 and 8% w/v polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.89→155.79 Å / Num. obs: 129546 / % possible obs: 98.8 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.5
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6388 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V7P

3v7p


Resolution: 1.89→28.591 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 6554 5.06 %
Rwork0.2311 122900 -
obs0.233 129454 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.65 Å2 / Biso mean: 26.6137 Å2 / Biso min: 12.21 Å2
Refinement stepCycle: final / Resolution: 1.89→28.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12828 0 140 985 13953
Biso mean--31.99 31.76 -
Num. residues----1637
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4736X-RAY DIFFRACTION2.39TORSIONAL
12B4736X-RAY DIFFRACTION2.39TORSIONAL
13C4736X-RAY DIFFRACTION2.39TORSIONAL
14D4736X-RAY DIFFRACTION2.39TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.89-1.91150.33861960.3141409497
1.9115-1.9340.3352040.2968404799
1.934-1.95760.35622200.28694119100
1.9576-1.98230.30012150.271413499
1.9823-2.00840.32222240.2765407399
2.0084-2.03590.3322510.2636408099
2.0359-2.0650.30792100.2644409599
2.065-2.09580.34332150.2665410799
2.0958-2.12850.30072310.2551406099
2.1285-2.16340.29212240.2518409199
2.1634-2.20070.33622190.2515409699
2.2007-2.24070.31621980.2537402997
2.2407-2.28380.27422010.2352397795
2.2838-2.33040.28532190.2402402599
2.3304-2.3810.27482200.23084100100
2.381-2.43640.29842040.23114210100
2.4364-2.49730.22512350.2196403599
2.4973-2.56480.27152150.2287411999
2.5648-2.64020.28312450.2338413699
2.6402-2.72540.30622230.2351409299
2.7254-2.82270.2842160.233411999
2.8227-2.93560.27762120.2346401796
2.9356-3.0690.24822240.2309403798
3.069-3.23060.26092220.2269411699
3.2306-3.43270.26642130.2337416999
3.4327-3.69730.26112200.2137413999
3.6973-4.06840.2392220.2063412898
4.0684-4.65490.24522180.2037404797
4.6549-5.85640.2691960.2314218100
5.8564-28.5910.23462420.2211419197

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