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- PDB-5tt8: Crystal structure of the complex of Helicobacter pylori alpha-car... -

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Basic information

Entry
Database: PDB / ID: 5tt8
TitleCrystal structure of the complex of Helicobacter pylori alpha-carbonic anhydrase with benzolamide
ComponentsAlpha-carbonic anhydrase
KeywordsLYASE / alpha-carbonic anhydrase / Helicobacter pylori / zinc metalloenzyme
Function / homology
Function and homology information


carbonic anhydrase / 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
Chem-D8W / carbonic anhydrase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 2, 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.pdbx_ptnr2_label_alt_id / _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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)219,01328
Polymers216,0138
Non-polymers3,00020
Water2,756153
1
A: Alpha-carbonic anhydrase
B: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8468
Polymers54,0032
Non-polymers8426
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)54,9028
Polymers54,0032
Non-polymers8996
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)54,4906
Polymers54,0032
Non-polymers4874
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)54,7756
Polymers54,0032
Non-polymers7724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.240, 134.400, 165.280
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
1GLUGLUGLUGLUchain AAA29 - 24516 - 232
2THRTHRARGARGchain BBB21 - 2478 - 234
3THRTHRARGARGchain CCC21 - 2478 - 234
4LYSLYSTHRTHRchain DDD28 - 24615 - 233
5LYSLYSARGARGchain EEE22 - 2479 - 234
6TRPTRPARGARGchain FFF23 - 24710 - 234
7ASNASNARGARGchain GGG20 - 2477 - 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
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, 173 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.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-D8W / 5-[(phenylsulfonyl)amino]-1,3,4-thiadiazole-2-sulfonamide


Mass: 320.369 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H8N4O4S3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.99 %
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: 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: 0.48
ReflectionResolution: 2.4→165.28 Å / Num. all: 55072 / Num. obs: 55072 / % possible obs: 78.3 % / Redundancy: 2.3 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.096 / Rsym value: 0.077 / Net I/av σ(I): 7.575 / Net I/σ(I): 8 / Num. measured all: 129205
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
2.4-2.532.20.3192.41860982880.2340.3980.3192.781.1
2.53-2.682.30.24831786777900.1790.3080.2483.480.4
2.68-2.872.30.1844.11690172970.1320.2280.1844.779.8
2.87-3.12.30.1395.41574667360.0990.1710.1396.279.4
3.1-3.392.40.10171457661490.0720.1250.1018.478.6
3.39-3.792.40.0769.11313354880.0550.0940.07611.277.3
3.79-4.382.40.05910.81147947650.0430.0730.0591476.7
4.38-5.372.40.04613966239650.0340.0570.04615.975.2
5.37-7.592.50.04513.2746830280.0330.0560.04514.573.5
7.59-42.6052.40.04612.3376415660.0350.0580.04617.868.5

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Processing

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

4ygf


Resolution: 2.4→41.32 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.67 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2313 3318 6.03 %
Rwork0.1984 52268 -
obs0.2031 55054 78.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.56 Å2 / Biso mean: 42.8139 Å2 / Biso min: 11.35 Å2
Refinement stepCycle: final / Resolution: 2.4→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14088 0 170 153 14411
Biso mean--37.52 28.62 -
Num. residues----1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114707
X-RAY DIFFRACTIONf_angle_d1.5519932
X-RAY DIFFRACTIONf_chiral_restr0.0712052
X-RAY DIFFRACTIONf_plane_restr0.0082580
X-RAY DIFFRACTIONf_dihedral_angle_d15.0735430
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8322X-RAY DIFFRACTION15.282TORSIONAL
12B8322X-RAY DIFFRACTION15.282TORSIONAL
13C8322X-RAY DIFFRACTION15.282TORSIONAL
14D8322X-RAY DIFFRACTION15.282TORSIONAL
15E8322X-RAY DIFFRACTION15.282TORSIONAL
16F8322X-RAY DIFFRACTION15.282TORSIONAL
17G8322X-RAY DIFFRACTION15.282TORSIONAL
18H8322X-RAY DIFFRACTION15.282TORSIONAL
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 (%)
2.4003-2.44170.30751220.2962735285778
2.4417-2.48610.28161360.27732650278677
2.4861-2.53390.31931360.27842713284977
2.5339-2.58560.34711360.28092752288877
2.5856-2.64180.28591270.26582602272976
2.6418-2.70330.28051590.26392667282676
2.7033-2.77080.31471330.26212710284377
2.7708-2.84570.26281460.25162618276475
2.8457-2.92950.27471450.23772694283975
2.9295-3.0240.29011380.23132569270775
3.024-3.1320.26521430.22282662280575
3.132-3.25740.23121490.22122585273475
3.2574-3.40560.22331330.20872638277174
3.4056-3.5850.23731420.19022566270874
3.585-3.80950.20651410.18242605274673
3.8095-4.10340.18671470.16592575272273
4.1034-4.51590.18261200.15492552267273
4.5159-5.16820.18981440.14242535267971
5.1682-6.50730.22471400.1712445258570
6.5073-41.32610.22831260.18722395252166

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