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- PDB-4rxy: Crystal Structure of the Beta Carbonic Anhydrase psCA3 isolated f... -

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Basic information

Entry
Database: PDB / ID: 4rxy
TitleCrystal Structure of the Beta Carbonic Anhydrase psCA3 isolated from Pseudomonas aeruginosa
ComponentsCarbonic anhydrase
KeywordsLYASE / reversible hydration
Function / homology
Function and homology information


cellular response to carbon dioxide / carbon utilization / carbonic anhydrase / carbonate dehydratase activity / cellular response to oxidative stress / zinc ion binding / cytoplasm
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsPinard, M.A. / Mckenna, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: Structure and inhibition studies of a type II beta-carbonic anhydrase psCA3 from Pseudomonas aeruginosa.
Authors: Pinard, M.A. / Lotlikar, S.R. / Boone, C.D. / Vullo, D. / Supuran, C.T. / Patrauchan, M.A. / McKenna, R.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4083
Polymers24,2511
Non-polymers1582
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,63212
Polymers97,0024
Non-polymers6308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area19070 Å2
ΔGint-247 kcal/mol
Surface area30550 Å2
MethodPISA
3
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8166
Polymers48,5012
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6610 Å2
ΔGint-115 kcal/mol
Surface area18200 Å2
MethodPISA
4
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8166
Polymers48,5012
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3220 Å2
ΔGint-83 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.241, 77.888, 87.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

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Components

#1: Protein Carbonic anhydrase


Mass: 24250.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4676 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HVB9, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.2 M ammonium sulfate, 0.1 M malic acid and 0.1 M imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 25, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 19179 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-1.97199.8
1.97-2.05199.9
2.05-2.14199.8
2.14-2.25199.4
2.25-2.39199.1
2.39-2.58198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→19.754 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 959 5 %5%
Rwork0.1649 ---
obs0.1662 19174 98.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.19 Å2 / Biso mean: 32.839 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: LAST / Resolution: 1.901→19.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 7 65 1739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081746
X-RAY DIFFRACTIONf_angle_d0.9942378
X-RAY DIFFRACTIONf_chiral_restr0.043272
X-RAY DIFFRACTIONf_plane_restr0.004306
X-RAY DIFFRACTIONf_dihedral_angle_d13.352644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.901-2.00160.25391360.21022570270699
2.0016-2.12680.23011370.182926182755100
2.1268-2.29080.19971390.17212626276599
2.2908-2.5210.1961350.16982582271799
2.521-2.88480.19451370.16822597273498
2.8848-3.63080.19021370.16582611274898
3.6308-19.75550.16881380.14792611274994
Refinement TLS params.Method: refined / Origin x: -27.263 Å / Origin y: -2.7721 Å / Origin z: -16.4819 Å
111213212223313233
T0.1762 Å2-0.0479 Å20.0381 Å2-0.1712 Å2-0.0066 Å2--0.1693 Å2
L0.4484 °2-0.028 °2-0.0536 °2-0.5006 °20.0274 °2--1.1481 °2
S-0.1543 Å °0.0904 Å °-0.0243 Å °-0.2329 Å °0.1041 Å °-0.1214 Å °0.0704 Å °0.2102 Å °-0.0333 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 211
2X-RAY DIFFRACTION1allA262 - 301
3X-RAY DIFFRACTION1allA1 - 465
4X-RAY DIFFRACTION1allA1 - 302

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