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- PDB-4ygf: Crystal structure of the complex of Helicobacter pylori alpha-Car... -

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Basic information

Entry
Database: PDB / ID: 4ygf
TitleCrystal structure of the complex of Helicobacter pylori alpha-Carbonic Anhydrase with acetazolamide
ComponentsAlpha-carbonic anhydrase
KeywordsLYASE / periplasm / zinc metalloenzyme
Function / homology
Function and homology information


regulation of pH / carbonate dehydratase activity / carbon dioxide transport / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Alpha-carbonic anhydrase / :
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRoujeinikova, A. / Modak, J.K.
CitationJournal: Plos One / Year: 2015
Title: Structural Basis for the Inhibition of Helicobacter pylori alpha-Carbonic Anhydrase by Sulfonamides.
Authors: Modakh, J.K. / Liu, Y.C. / Machuca, M.A. / Supuran, C.T. / Roujeinikova, A.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Data collection
Revision 1.2Dec 16, 2015Group: Structure summary
Revision 1.3Sep 27, 2023Group: 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-carbonic anhydrase
B: Alpha-carbonic anhydrase
C: Alpha-carbonic anhydrase
D: Alpha-carbonic anhydrase
E: Alpha-carbonic anhydrase
F: Alpha-carbonic anhydrase
G: Alpha-carbonic anhydrase
H: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,05837
Polymers216,0138
Non-polymers3,04529
Water18,3571019
1
A: Alpha-carbonic anhydrase
B: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7429
Polymers54,0032
Non-polymers7387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-carbonic anhydrase
D: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7429
Polymers54,0032
Non-polymers7387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Alpha-carbonic anhydrase
F: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7429
Polymers54,0032
Non-polymers7387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Alpha-carbonic anhydrase
H: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,83410
Polymers54,0032
Non-polymers8308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.780, 133.610, 166.540
Angle α, β, γ (deg.)90.000, 90.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid A
41chain D and segid B
51chain E and segid A
61chain F and segid B
71chain G and segid A
81chain H and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid AC0
411chain D and segid BD0
511chain E and segid AE0
611chain F and segid BF0
711chain G and segid AG0
811chain H and segid BH0

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Alpha-carbonic anhydrase


Mass: 27001.596 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: C694_06140 / Production host: Escherichia coli (E. coli) / References: UniProt: K4NGD4, UniProt: A0A0M3KL20*PLUS

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Non-polymers , 5 types, 1048 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24% (w/v) PEG 1.5K, 200 mM di-basic ammonium citrate, 2 mM zinc chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2→166.539 Å / Num. all: 119874 / Num. obs: 119874 / % possible obs: 97.6 % / Redundancy: 3.4 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.113 / Rsym value: 0.096 / Net I/av σ(I): 5.372 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.113.20.247352686164850.1550.2473.692.6
2.11-2.243.20.213.552110162040.1330.214.395.8
2.24-2.393.30.183.951064156220.1130.184.998.1
2.39-2.583.40.1514.550475147690.0940.151699.3
2.58-2.833.60.1245.348173135560.0760.1247.599.5
2.83-3.163.70.1046.344902123010.0630.1049.799.6
3.16-3.653.70.092740179108910.0550.09212.399.7
3.65-4.473.70.0778.13374692100.0470.07713.999.7
4.47-6.323.60.0698.62574171480.0420.06913.699.6
6.32-32.5683.30.05610.91232136880.0360.05612.792.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4g7a

4g7a


Resolution: 2→32.568 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.84 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2149 6157 5.14 %
Rwork0.1869 113680 -
obs0.1908 119722 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.54 Å2 / Biso mean: 27.933 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 2→32.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14762 0 150 1019 15931
Biso mean--21.67 24.32 -
Num. residues----1804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115394
X-RAY DIFFRACTIONf_angle_d1.42420849
X-RAY DIFFRACTIONf_chiral_restr0.0622146
X-RAY DIFFRACTIONf_plane_restr0.0072707
X-RAY DIFFRACTIONf_dihedral_angle_d14.1015752
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8889X-RAY DIFFRACTION14.199TORSIONAL
12B8889X-RAY DIFFRACTION14.199TORSIONAL
13C8889X-RAY DIFFRACTION14.199TORSIONAL
14D8889X-RAY DIFFRACTION14.199TORSIONAL
15E8889X-RAY DIFFRACTION14.199TORSIONAL
16F8889X-RAY DIFFRACTION14.199TORSIONAL
17G8889X-RAY DIFFRACTION14.199TORSIONAL
18H8889X-RAY DIFFRACTION14.199TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.00010.29482850.27655278556387
2.0346-2.07160.2752430.26285401564488
2.0716-2.11140.25183050.26795401570688
2.1114-2.15450.30882930.2625500579390
2.1545-2.20130.28513080.25415613592190
2.2013-2.25250.28152870.25865560584792
2.2525-2.30880.26423030.25645710601392
2.3088-2.37120.25432530.25295730598394
2.3712-2.44090.25842870.24855795608294
2.4409-2.51970.27763030.23845741604494
2.5197-2.60960.26613150.23695843615894
2.6096-2.7140.26673210.22655709603094
2.714-2.83740.26683270.21425751607894
2.8374-2.98680.22153170.19795866618394
2.9868-3.17360.21493300.18355765609594
3.1736-3.41820.20523190.16995799611894
3.4182-3.76120.16953110.14595845615695
3.7612-4.30340.16493040.12845804610895
4.3034-5.41380.15392830.11995884616795
5.4138-26.09170.18773100.16065685599591

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