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- PDB-5tt3: Crystal structure of the complex of Helicobacter pylori alpha-car... -

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Basic information

Entry
Database: PDB / ID: 5tt3
TitleCrystal structure of the complex of Helicobacter pylori alpha-carbonic anhydrase with ethoxzolamide
ComponentsAlpha-carbonic anhydrase
KeywordsLYASE / alpha-carbonic anhydrase / Helicobacter pylori / zinc metalloenzyme / zinc / periplasm
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
6-ethoxy-1,3-benzothiazole-2-sulfonamide / Alpha-carbonic anhydrase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1, 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)219,01734
Polymers216,0138
Non-polymers3,00526
Water9,638535
1
A: Alpha-carbonic anhydrase
B: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,90610
Polymers54,0032
Non-polymers9038
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)54,5207
Polymers54,0032
Non-polymers5175
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)54,7788
Polymers54,0032
Non-polymers7756
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)54,8149
Polymers54,0032
Non-polymers8107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.980, 138.860, 168.180
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
1LYSLYSARGARGchain AAA22 - 2479 - 234
2LYSLYSARGARGchain BBB22 - 2479 - 234
3THRTHRARGARGchain CCC21 - 2478 - 234
4TRPTRPTHRTHRchain DDD23 - 24610 - 233
5LYSLYSARGARGchain EEE22 - 2479 - 234
6TRPTRPARGARGchain FFF23 - 24710 - 234
7THRTHRARGARGchain GGG21 - 2478 - 234
8TRPTRPARGARGchain HHH23 - 24710 - 234

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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 / Mutation: N-terminal extension GIDFPT (cloning artefact)
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

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Non-polymers , 5 types, 561 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.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EZL / 6-ethoxy-1,3-benzothiazole-2-sulfonamide / Ethoxzolamide


Mass: 258.317 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H10N2O3S2 / Comment: medication, inhibitor*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.: 535 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
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 zinc chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2016
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: 0.5
ReflectionResolution: 2.2→168.18 Å / Num. all: 96783 / Num. obs: 96783 / % possible obs: 97.1 % / Redundancy: 2.9 % / Rpim(I) all: 0.045 / Rrim(I) all: 0.081 / Rsym value: 0.067 / Net I/av σ(I): 8.687 / Net I/σ(I): 9.8 / Num. measured all: 282181
Reflection shell

Diffraction-ID: 1 / Rejects: _

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
2.2-2.322.90.4911.541558142800.3380.5990.4912.498.5
2.32-2.462.90.3552.139478135290.2440.4330.3553.298.3
2.46-2.632.90.2323.237108127120.1590.2820.2324.598.2
2.63-2.842.90.1415.334295117120.0960.1710.1416.697.3
2.84-3.112.90.098.131528107740.0610.1090.099.497.3
3.11-3.482.90.0669.82828897870.0450.080.06613.497.8
3.48-4.022.90.05111.92464985090.0340.0620.05118.296.2
4.02-4.922.70.03218.91928670670.0220.0390.03221.794.6
4.92-6.963.10.04413.11693755000.0280.0520.04422.394.6
6.96-39.8933.10.02820.9905429130.0190.0340.0282691

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ygf


Resolution: 2.2→39.893 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2403 4875 5.04 %
Rwork0.2022 91851 -
obs0.206 96747 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.84 Å2 / Biso mean: 44.7328 Å2 / Biso min: 12.53 Å2
Refinement stepCycle: final / Resolution: 2.2→39.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14322 0 156 535 15013
Biso mean--38.49 35.29 -
Num. residues----1751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114974
X-RAY DIFFRACTIONf_angle_d1.43520291
X-RAY DIFFRACTIONf_chiral_restr0.0612098
X-RAY DIFFRACTIONf_plane_restr0.0072621
X-RAY DIFFRACTIONf_dihedral_angle_d14.2385568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8503X-RAY DIFFRACTION13.194TORSIONAL
12B8503X-RAY DIFFRACTION13.194TORSIONAL
13C8503X-RAY DIFFRACTION13.194TORSIONAL
14D8503X-RAY DIFFRACTION13.194TORSIONAL
15E8503X-RAY DIFFRACTION13.194TORSIONAL
16F8503X-RAY DIFFRACTION13.194TORSIONAL
17G8503X-RAY DIFFRACTION13.194TORSIONAL
18H8503X-RAY DIFFRACTION13.194TORSIONAL
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 (%)
2.2-2.23790.29552550.28494681493694
2.2379-2.27860.29472600.27944548480891
2.2786-2.32240.31842610.28234644490594
2.3224-2.36970.26872390.27864677491693
2.3697-2.42120.27682520.27734553480592
2.4212-2.47740.31992400.27064725496595
2.4774-2.53930.2792220.26724570479291
2.5393-2.60790.26212310.26794676490795
2.6079-2.68450.3142380.26894615485391
2.6845-2.7710.2992500.25434618486894
2.771-2.86990.28152230.24884619484291
2.8699-2.98460.28822510.23684616486794
2.9846-3.12010.2432320.2254590482291
3.1201-3.28420.24732460.21644585483192
3.2842-3.48930.23862330.20194657489093
3.4893-3.75770.22372550.18274546480191
3.7577-4.13390.22142530.15884538479191
4.1339-4.72760.18882430.14354479472289
4.7276-5.93960.19592310.15114440467189
5.9396-23.14380.22192290.17834474470388

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