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- PDB-5tv3: Crystal structure of the complex of Helicobacter pylori alpha-car... -

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Basic information

Entry
Database: PDB / ID: 5tv3
TitleCrystal structure of the complex of Helicobacter pylori alpha-carbonic anhydrase with (E)-5-(((4-(tert-butyl)phenyl)sulfonyl)imino)-4-methyl-4,5-dihydro-1,3,4-thiadiazole-2-sulfonamide
ComponentsAlpha-carbonic anhydrase
KeywordsLYASE/LYASE inhibitor / alpha-carbonic anhydrase / Helicobacter pylori / lyase / zinc-metalloenzyme / 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
Chem-7L3 / Alpha-carbonic anhydrase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 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)219,82327
Polymers216,0138
Non-polymers3,81019
Water0
1
A: Alpha-carbonic anhydrase
B: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9156
Polymers54,0032
Non-polymers9124
Water0
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)55,0438
Polymers54,0032
Non-polymers1,0396
Water0
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)54,9156
Polymers54,0032
Non-polymers9124
Water0
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)54,9507
Polymers54,0032
Non-polymers9475
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.560, 133.890, 166.600
Angle α, β, γ (deg.)90.000, 90.300, 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 / End auth comp-ID: ARG / End label comp-ID: ARG

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSchain AAA22 - 2479 - 234
2LYSLYSchain BBB22 - 2479 - 234
3TRPTRPchain CCC23 - 24710 - 234
4TRPTRPchain DDD23 - 24710 - 234
5LYSLYSchain EEE22 - 2479 - 234
6TRPTRPchain FFF23 - 24710 - 234
7ASNASNchain GGG20 - 2477 - 234
8TRPTRPchain 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-7L3 / (5Z)-5-{[(4-tert-butylphenyl)sulfonyl]imino}-4-methyl-4,5-dihydro-1,3,4-thiadiazole-2-sulfonamide


Mass: 390.501 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H18N4O4S3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 42.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: Dec 17, 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: 0.5
ReflectionResolution: 2.9→166.598 Å / Num. all: 39929 / Num. obs: 39929 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rpim(I) all: 0.067 / Rrim(I) all: 0.127 / Rsym value: 0.108 / Net I/av σ(I): 5.4 / Net I/σ(I): 8.3 / Num. measured all: 138343
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
2.9-3.063.50.2652.72062358570.1640.3130.265499.7
3.06-3.243.50.1983.61957055620.1230.2340.1985.399.8
3.24-3.473.50.1564.51847752660.0960.1830.1566.899.6
3.47-3.743.50.1265.41679548030.0780.1480.1268.599.1
3.74-4.13.50.1136.11542944180.0690.1330.1139.898.7
4.1-4.593.50.16.51395539950.0610.1170.111.398.1
4.59-5.293.30.0876.91143034880.0550.1030.08711.397.7
5.29-6.482.90.0777.6843128830.0520.0940.0779.895.3
6.48-9.173.80.0718.4893423740.0430.0830.07112.4100
9.17-29.943.70.0728469912830.0440.0850.07214.196.5

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Processing

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

4ygf


Resolution: 2.9→29.94 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.68 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2426 2052 5.14 %
Rwork0.1871 37815 -
obs0.1924 39892 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.58 Å2 / Biso mean: 44.9182 Å2 / Biso min: 12.34 Å2
Refinement stepCycle: final / Resolution: 2.9→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14599 0 208 0 14807
Biso mean--39.91 --
Num. residues----1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115273
X-RAY DIFFRACTIONf_angle_d1.65120717
X-RAY DIFFRACTIONf_chiral_restr0.0712112
X-RAY DIFFRACTIONf_plane_restr0.0082678
X-RAY DIFFRACTIONf_dihedral_angle_d13.9085670
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8769X-RAY DIFFRACTION13.115TORSIONAL
12B8769X-RAY DIFFRACTION13.115TORSIONAL
13C8769X-RAY DIFFRACTION13.115TORSIONAL
14D8769X-RAY DIFFRACTION13.115TORSIONAL
15E8769X-RAY DIFFRACTION13.115TORSIONAL
16F8769X-RAY DIFFRACTION13.115TORSIONAL
17G8769X-RAY DIFFRACTION13.115TORSIONAL
18H8769X-RAY DIFFRACTION13.115TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9006-2.9730.32241560.29492782293894
2.973-3.05320.26711390.26872645278495
3.0532-3.14280.29991170.2572753287096
3.1428-3.24390.29351580.23782697285594
3.2439-3.35950.28491370.23562691282895
3.3595-3.49350.27851770.22232720289793
3.4935-3.65180.27551420.20882664280694
3.6518-3.84340.25921310.19072718284994
3.8434-4.08280.20971540.17652677283193
4.0828-4.39580.2591240.1642676280094
4.3958-4.8340.18151450.14712688283393
4.834-5.52390.19291430.15252666280993
5.5239-6.92390.25081470.16612670281791
6.9239-22.11810.21461310.16082768289995

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