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- PDB-5jj8: Crystal Structure of the Beta Carbonic Anhydrase psCA3 isolated f... -

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Basic information

Entry
Database: PDB / ID: 5jj8
TitleCrystal Structure of the Beta Carbonic Anhydrase psCA3 isolated from Pseudomonas aeruginosa - alternate crystal packing form
ComponentsCarbonic anhydrase
KeywordsLYASE / psCA3 / crystal packing / beta-carbonic anhydrase
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
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
Carbonic anhydrase / Carbonic anhydrase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.585 Å
AuthorsPinard, M.A. / Kurian, J.J. / Aggarwal, M. / Agbandje-McKenna, M. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM25154 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Cryoannealing-induced space-group transition of crystals of the carbonic anhydrase psCA3.
Authors: Pinard, M.A. / Kurian, J.J. / Aggarwal, M. / Agbandje-McKenna, M. / McKenna, R.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6324
Polymers48,5012
Non-polymers1312
Water39622
1
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6324
Polymers48,5012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area5960 Å2
ΔGint-112 kcal/mol
Surface area18250 Å2
MethodPISA
2
B: Carbonic anhydrase
hetero molecules

B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6324
Polymers48,5012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544x,-y-1,-z-11
Buried area5990 Å2
ΔGint-114 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.429, 69.362, 77.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21B-409-

HOH

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Components

#1: Protein Carbonic anhydrase / Carbonate dehydratase


Mass: 24250.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: can_1, can, yadF, AO943_21535, AO946_10560, AOD73_25440, AOU28_24465, AOY09_00950, APT60_24635, ATC05_14980, AU380_02155, ERS445055_04974, HV95_21180, HV96_01220, HV97_23895, HV98_01810, HV99_ ...Gene: can_1, can, yadF, AO943_21535, AO946_10560, AOD73_25440, AOU28_24465, AOY09_00950, APT60_24635, ATC05_14980, AU380_02155, ERS445055_04974, HV95_21180, HV96_01220, HV97_23895, HV98_01810, HV99_02890, HW00_06825, HW01_20790, HW02_08065, HW03_11820, HW04_25045, HW05_22660, HW06_00905, HW07_08265, HW08_30020, HW09_16360, HW10_17975, IOMTU133_5488, PA257_5879, PA8380_53220, PAERUG_E15_London_28_01_14_01862, PAERUG_P32_London_17_VIM_2_10_11_05532, PAO1OR4768
Production host: Escherichia coli (E. coli)
References: UniProt: A0A072ZBL6, UniProt: Q9HVB9*PLUS, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Hampton Research Crystal Screen 2, PEG/Ion, PEG/Ion 2, an in-house sodium citrate screen (screening conditions varied from 1.1 to 1.8 M sodium citrate, Tris-HCl pH 7.1-8.1), and an in-house ...Details: Hampton Research Crystal Screen 2, PEG/Ion, PEG/Ion 2, an in-house sodium citrate screen (screening conditions varied from 1.1 to 1.8 M sodium citrate, Tris-HCl pH 7.1-8.1), and an in-house ammonium sulfate screen (screening conditions varied from 1.8 M to 2.8 M ammonium sulfate, 0.1 M malic acid, 0.1 M imidazole pH 7.0-8.5) prepared by the Rigaku Alchemist DT were used to screen for optimum crystallization conditions.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9177 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionResolution: 2.585→35.553 Å / Num. obs: 14191 / % possible obs: 91.48 % / Redundancy: 3.2 % / Net I/σ(I): 17.3

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RXY

4rxy


Resolution: 2.585→35.553 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.09
RfactorNum. reflection% reflection
Rfree0.2751 710 5 %
Rwork0.2117 --
obs0.2148 14191 91.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.585→35.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 2 22 3336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093468
X-RAY DIFFRACTIONf_angle_d1.2434730
X-RAY DIFFRACTIONf_dihedral_angle_d14.6891272
X-RAY DIFFRACTIONf_chiral_restr0.057544
X-RAY DIFFRACTIONf_plane_restr0.007610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5849-2.78440.30711200.22892278X-RAY DIFFRACTION79
2.7844-3.06450.35291300.24082472X-RAY DIFFRACTION85
3.0645-3.50760.3441530.23612901X-RAY DIFFRACTION99
3.5076-4.41790.24951530.19272908X-RAY DIFFRACTION99
4.4179-35.55670.23811540.20292922X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 16.6609 Å / Origin y: -9.0053 Å / Origin z: -16.6188 Å
111213212223313233
T0.3762 Å2-0.0359 Å2-0.0219 Å2-0.3194 Å20.1536 Å2--0.3574 Å2
L1.2072 °20.7675 °20.7557 °2-0.57 °20.6288 °2--0.7856 °2
S-0.0794 Å °0.0161 Å °0.2271 Å °-0.0605 Å °-0.0623 Å °0.1049 Å °-0.0351 Å °0.0362 Å °-0.0036 Å °
Refinement TLS groupSelection details: all

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