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

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Basic information

Entry
Database: PDB / ID: 4yha
TitleCrystal structure of the complex of Helicobacter pylori alpha-Carbonic Anhydrase with methazolamide
ComponentsAlpha-carbonic anhydrase
KeywordsLYASE / zinc metalloenzyme / methazolamide
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-MZM / Alpha-carbonic anhydrase / :
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Structure summary
Revision 2.0Nov 22, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / pdbx_struct_oper_list / software
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.1Sep 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 / pdbx_initial_refinement_model / struct_conn
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

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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)219,00734
Polymers216,0138
Non-polymers2,99526
Water10,539585
1
A: Alpha-carbonic anhydrase
B: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6778
Polymers54,0032
Non-polymers6746
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)54,8269
Polymers54,0032
Non-polymers8237
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)54,7348
Polymers54,0032
Non-polymers7316
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)54,7709
Polymers54,0032
Non-polymers7667
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.450, 135.650, 166.580
Angle α, β, γ (deg.)90.000, 90.050, 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, 611 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-MZM / N-(3-methyl-5-sulfamoyl-1,3,4-thiadiazol-2(3H)-ylidene)acetamide / Methazolamide


Mass: 236.272 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H8N4O3S2 / Comment: inhibitor*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
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: MX2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.2→166.58 Å / Num. all: 93672 / Num. obs: 93672 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.091 / Rsym value: 0.078 / Net I/av σ(I): 5.337 / Net I/σ(I): 11 / Num. measured all: 351477
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
2.2-2.323.80.2133.451944135620.1260.2135.397.7
2.32-2.463.80.1694.249173129000.10.1696.497.9
2.46-2.633.80.1345.246180121650.0790.1347.998.3
2.63-2.843.80.1046.242975113530.0620.1049.998.4
2.84-3.113.80.0866.839152104070.0520.0861298.6
3.11-3.483.70.0737.73528094740.0440.07314.498.7
3.48-4.023.70.0697.93082183310.0410.06916.498.6
4.02-4.923.60.0667.92511970710.040.06617.498.5
4.92-6.963.60.06481929753870.0390.06416.896.5
6.96-29.9033.80.068.81153630220.0360.0618.598

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
Cootmodel building
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G7A

4g7a


Resolution: 2.2→29.903 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2448 4792 5.12 %
Rwork0.2077 88897 -
obs0.2119 93642 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 257.31 Å2 / Biso mean: 36.6055 Å2 / Biso min: 9.67 Å2
Refinement stepCycle: final / Resolution: 2.2→29.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14581 0 150 585 15316
Biso mean--34.98 28.39 -
Num. residues----1782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115198
X-RAY DIFFRACTIONf_angle_d1.45120584
X-RAY DIFFRACTIONf_chiral_restr0.0642120
X-RAY DIFFRACTIONf_plane_restr0.0072667
X-RAY DIFFRACTIONf_dihedral_angle_d14.0595658
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8727X-RAY DIFFRACTION15.87TORSIONAL
12B8727X-RAY DIFFRACTION15.87TORSIONAL
13C8727X-RAY DIFFRACTION15.87TORSIONAL
14D8727X-RAY DIFFRACTION15.87TORSIONAL
15E8727X-RAY DIFFRACTION15.87TORSIONAL
16F8727X-RAY DIFFRACTION15.87TORSIONAL
17G8727X-RAY DIFFRACTION15.87TORSIONAL
18H8727X-RAY DIFFRACTION15.87TORSIONAL
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 (%)
2.2-2.20010.34552470.3034450469792
2.238-2.27860.31632060.29464340454693
2.2786-2.32240.32782370.28984443468093
2.3224-2.36980.29082380.28584446468493
2.3698-2.42130.33122170.27524391460893
2.4213-2.47750.28352490.27734446469593
2.4775-2.53940.3012350.27624393462893
2.5394-2.6080.311940.28364474466894
2.608-2.68460.27442180.26524495471394
2.6846-2.77110.3032070.25784470467794
2.7711-2.870.28112240.24564464468894
2.87-2.98470.27772330.23984414464793
2.9847-3.12030.26212470.22334457470494
3.1203-3.28440.24752560.21774483473993
3.2844-3.48950.23212470.20074445469294
3.4895-3.75790.21192580.18284439469793
3.7579-4.13420.20382350.16624459469493
4.1342-4.72820.17562710.14524490476193
4.7282-5.9410.22142090.1554357456691
5.941-23.44050.23972750.1784541481694

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