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

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Basic information

Entry
Database: PDB / ID: 7lkj
TitleCrystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA)
ComponentsAminofutalosine deaminase
KeywordsHYDROLASE / Aminofutalosine deaminase / AFLDA / Inhibitor / Inhibitor complex / H. pylori
Function / homology: / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / metal ion binding / : / Putative
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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

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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)190,55812
Polymers190,0814
Non-polymers4788
Water2,684149
1
A: Aminofutalosine deaminase
B: Aminofutalosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4629
Polymers95,0402
Non-polymers4227
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-32 kcal/mol
Surface area30700 Å2
MethodPISA
2
C: Aminofutalosine deaminase
D: Aminofutalosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0963
Polymers95,0402
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-25 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.295, 73.295, 157.495
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 28 or (resid 29...
21(chain B and (resid 1 through 69 or resid 75...
31(chain C and (resid 1 through 28 or (resid 29...
41(chain D and (resid 1 through 28 or (resid 29...

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
11METMETASPASP(chain A and (resid 1 through 28 or (resid 29...AA1 - 2815 - 42
12GLUGLULYSLYS(chain A and (resid 1 through 28 or (resid 29...AA29 - 3043 - 44
13METMETILEILE(chain A and (resid 1 through 28 or (resid 29...AA1 - 40915 - 423
14METMETILEILE(chain A and (resid 1 through 28 or (resid 29...AA1 - 40915 - 423
15METMETILEILE(chain A and (resid 1 through 28 or (resid 29...AA1 - 40915 - 423
16METMETILEILE(chain A and (resid 1 through 28 or (resid 29...AA1 - 40915 - 423
21METMETGLUGLU(chain B and (resid 1 through 69 or resid 75...BB1 - 6915 - 83
22ALAALALEULEU(chain B and (resid 1 through 69 or resid 75...BB75 - 11289 - 126
23LYSLYSLYSLYS(chain B and (resid 1 through 69 or resid 75...BB113127
24METMETILEILE(chain B and (resid 1 through 69 or resid 75...BB1 - 40915 - 423
25METMETILEILE(chain B and (resid 1 through 69 or resid 75...BB1 - 40915 - 423
26METMETILEILE(chain B and (resid 1 through 69 or resid 75...BB1 - 40915 - 423
27METMETILEILE(chain B and (resid 1 through 69 or resid 75...BB1 - 40915 - 423
31METMETASPASP(chain C and (resid 1 through 28 or (resid 29...CC1 - 2815 - 42
32GLUGLULYSLYS(chain C and (resid 1 through 28 or (resid 29...CC29 - 3043 - 44
33METMETILEILE(chain C and (resid 1 through 28 or (resid 29...CC1 - 40915 - 423
34METMETILEILE(chain C and (resid 1 through 28 or (resid 29...CC1 - 40915 - 423
35METMETILEILE(chain C and (resid 1 through 28 or (resid 29...CC1 - 40915 - 423
36METMETILEILE(chain C and (resid 1 through 28 or (resid 29...CC1 - 40915 - 423
41METMETASPASP(chain D and (resid 1 through 28 or (resid 29...DD1 - 2815 - 42
42GLUGLULYSLYS(chain D and (resid 1 through 28 or (resid 29...DD29 - 3043 - 44
43METMETILEILE(chain D and (resid 1 through 28 or (resid 29...DD1 - 40915 - 423
44METMETILEILE(chain D and (resid 1 through 28 or (resid 29...DD1 - 40915 - 423
45METMETILEILE(chain D and (resid 1 through 28 or (resid 29...DD1 - 40915 - 423
46METMETILEILE(chain D and (resid 1 through 28 or (resid 29...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.: 3 / Source method: isolated from a natural source / Formula: Fe
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM Sodium malonate pH 4.0 and 12% w/v polyethylene glycol 3,350

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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: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.79→155.73 Å / Num. obs: 39040 / % possible obs: 94.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5
Reflection shellResolution: 2.79→2.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4432 / CC1/2: 0.55

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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: 2.79→155.727 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 1997 5.12 %
Rwork0.2525 37009 -
obs0.2543 39006 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.97 Å2 / Biso mean: 41.1664 Å2 / Biso min: 24.95 Å2
Refinement stepCycle: final / Resolution: 2.79→155.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12564 0 23 151 12738
Biso mean--46.93 30.47 -
Num. residues----1615
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4744X-RAY DIFFRACTION1.909TORSIONAL
12B4744X-RAY DIFFRACTION1.909TORSIONAL
13C4744X-RAY DIFFRACTION1.909TORSIONAL
14D4744X-RAY DIFFRACTION1.909TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7901-2.85980.39931290.342261194
2.8598-2.93720.36961320.3427275697
2.9372-3.02360.3821240.3281272498
3.0236-3.12120.42281420.3138270097
3.1212-3.23280.32821380.2881276198
3.2328-3.36220.35521600.2719274898
3.3622-3.51520.29631170.2645196671
3.5152-3.70060.32311140.2482238184
3.7006-3.93250.26271640.2395239287
3.9325-4.23610.27181700.22276599
4.2361-4.66240.2411530.2183272297
4.6624-5.33710.25471670.2117278899
5.3371-6.72430.2871340.2508284599
6.7243-155.7270.22581530.223285098
Refinement TLS params.Method: refined / Origin x: 12.2035 Å / Origin y: 24.2803 Å / Origin z: 38.9466 Å
111213212223313233
T0.2333 Å2-0.0177 Å2-0.051 Å2-0.2519 Å2-0.0081 Å2--0.5177 Å2
L0.0073 °2-0.0908 °2-0.036 °2--0.043 °20.0431 °2--0.241 °2
S-0.0034 Å °-0.038 Å °0.0127 Å °-0.0235 Å °-0.0074 Å °0.0036 Å °-0.0018 Å °-0.0092 Å °0.0165 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 409
2X-RAY DIFFRACTION1allB1 - 409
3X-RAY DIFFRACTION1allC1 - 409
4X-RAY DIFFRACTION1allD1 - 409
5X-RAY DIFFRACTION1allW1 - 151
6X-RAY DIFFRACTION1allE1 - 3
7X-RAY DIFFRACTION1allF501 - 901

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