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- PDB-5tuo: Crystal structure of the complex of Helicobacter pylori alpha-car... -

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Basic information

Entry
Database: PDB / ID: 5tuo
TitleCrystal structure of the complex of Helicobacter pylori alpha-carbonic anhydrase with 5-amino-1,3,4-thiadiazole-2-sulfonamide inhibitor.
ComponentsAlpha-carbonic anhydrase
KeywordsLYASE/LYASE inhibitor / lyase / alpha-carbonic anhydrase / Helicobacter pylori / zinc metalloenzyme / 5-amino-1 / 3 / 4-thiadiazole-2-sulfonamide / LYASE-LYASE inhibitor complex
Function / homology
Function and homology information


carbonate dehydratase activity / 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-AMINO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Alpha-carbonic anhydrase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsModak, J.K. / Roujeinikova, A.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Structure-Activity Relationship for Sulfonamide Inhibition of Helicobacter pylori alpha-Carbonic Anhydrase.
Authors: Modak, J.K. / Liu, Y.C. / Supuran, C.T. / Roujeinikova, A.
History
DepositionNov 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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: 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)218,22631
Polymers216,0138
Non-polymers2,21323
Water1,856103
1
A: Alpha-carbonic anhydrase
B: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5658
Polymers54,0032
Non-polymers5626
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)54,5658
Polymers54,0032
Non-polymers5626
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)54,5307
Polymers54,0032
Non-polymers5275
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)54,5658
Polymers54,0032
Non-polymers5626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.840, 136.920, 166.270
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRARGARGchain AAA21 - 2478 - 234
2LYSLYSARGARGchain BBB22 - 2479 - 234
3LYSLYSARGARGchain CCC22 - 2479 - 234
4TRPTRPARGARGchain DDD23 - 24710 - 234
5ASNASNARGARGchain EEE20 - 2477 - 234
6TRPTRPTHRTHRchain FFF23 - 24610 - 233
7THRTHRARGARGchain GGG21 - 2478 - 234
8TRPTRPARGARGchain HHH23 - 24710 - 234

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Components

#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 (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: C694_06140
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0M3KL20, carbonic anhydrase
#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 / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-1SA / 5-AMINO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 180.209 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4N4O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% (w/v) PEG 1.5K, 100 mM di-basic ammonium citrate, 1 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 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: 0.9537 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.15
ReflectionResolution: 2.5→166.27 Å / Num. all: 64612 / Num. obs: 64612 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Rsym value: 0.047 / Net I/av σ(I): 13.2 / Net I/σ(I): 16.6 / Num. measured all: 213336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.643.10.3152.32936494450.2120.3820.3153.799.7
2.64-2.83.10.2043.62782689100.1380.2480.2045.599.9
2.8-2.993.20.1365.42671783910.0910.1640.1367.999.9
2.99-3.233.20.0888.32489477840.0590.1060.0881299.9
3.23-3.543.30.05911.92326671340.0390.0710.05917.799.9
3.54-3.953.40.045152221264980.0290.0540.04524.399.9
3.95-4.563.60.03320.12101057690.020.0380.03332.199.9
4.56-5.593.70.02723.51767848320.0160.0320.02734.199.9
5.59-7.913.60.02823.91363737960.0170.0330.02831.599.8
7.91-29.9123.30.02522.7673220530.0170.030.02537.497.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHENIXphasing
ADSCdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YGF

4ygf


Resolution: 2.5→29.912 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2721 3277 5.07 %
Rwork0.2269 61286 -
obs0.229 64588 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.94 Å2 / Biso mean: 52.3148 Å2 / Biso min: 18.91 Å2
Refinement stepCycle: final / Resolution: 2.5→29.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14347 0 95 103 14545
Biso mean--47.09 37 -
Num. residues----1755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114873
X-RAY DIFFRACTIONf_angle_d1.33720132
X-RAY DIFFRACTIONf_chiral_restr0.0522081
X-RAY DIFFRACTIONf_plane_restr0.0062611
X-RAY DIFFRACTIONf_dihedral_angle_d16.2915507
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8431X-RAY DIFFRACTION19.393TORSIONAL
12B8431X-RAY DIFFRACTION19.393TORSIONAL
13C8431X-RAY DIFFRACTION19.393TORSIONAL
14D8431X-RAY DIFFRACTION19.393TORSIONAL
15E8431X-RAY DIFFRACTION19.393TORSIONAL
16F8431X-RAY DIFFRACTION19.393TORSIONAL
17G8431X-RAY DIFFRACTION19.393TORSIONAL
18H8431X-RAY DIFFRACTION19.393TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5003-2.54340.36421520.33363089324195
2.5434-2.58960.38681750.33753053322894
2.5896-2.63940.38171730.33773041321494
2.6394-2.69320.35211580.31893015317395
2.6932-2.75170.39751600.31983084324495
2.7517-2.81570.40291580.31473099325795
2.8157-2.8860.39321560.30772974313095
2.886-2.96390.32121730.29733117329095
2.9639-3.0510.35991540.28593020317495
3.051-3.14940.32171590.26993066322595
3.1494-3.26180.30391730.26173084325795
3.2618-3.39210.2811570.24332996315395
3.3921-3.54620.28471520.22263129328195
3.5462-3.73270.23681890.20763032322194
3.7327-3.96590.26071580.20813048320695
3.9659-4.2710.20861590.18533083324295
4.271-4.69880.2431680.16833098326695
4.6988-5.37410.24041630.17933059322295
5.3741-6.75320.21741570.20933095325295
6.7532-27.02160.22261760.18323104328094

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