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- PDB-1i6o: CRYSTAL STRUCTURE OF E. COLI BETA CARBONIC ANHYDRASE (ECCA) -

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Basic information

Entry
Database: PDB / ID: 1i6o
TitleCRYSTAL STRUCTURE OF E. COLI BETA CARBONIC ANHYDRASE (ECCA)
ComponentsCARBONIC ANHYDRASE
KeywordsLYASE / carbonic anhydrase / metalloenzyme / zinc coordination / pH-dependent activity / MAD phasing
Function / homology
Function and homology information


cellular response to carbon dioxide / carbon utilization / carbonic anhydrase / carbonate dehydratase activity / cellular response to oxidative stress / protein homotetramerization / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 1. / 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 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsCronk, J.D. / Endrizzi, J.A. / Cronk, M.R. / O'Neill, J.W. / Zhang, K.Y.J.
Citation
Journal: Protein Sci. / Year: 2001
Title: Crystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity.
Authors: Cronk, J.D. / Endrizzi, J.A. / Cronk, M.R. / O'neill, J.W. / Zhang, K.Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Cloning, crystallization and preliminary characterization of a beta carbonic anhydrase from Escherichia coli
Authors: Cronk, J.D. / O'Neill, J.W. / Cronk, M.R. / Endrizzi, J.A. / Zhang, K.Y.J.
History
DepositionMar 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 99DENSITY FOR THE FOLLOWING ATOMS WITHIN THE MAIN CHAIN IS RELATIVELY WEAK AND LIKELY REFLECTS ...DENSITY FOR THE FOLLOWING ATOMS WITHIN THE MAIN CHAIN IS RELATIVELY WEAK AND LIKELY REFLECTS INCREASED LOCAL CONFORMATIONAL FLEXIBILITY OF THE MAIN CHAIN IN THIS REGION. ALA A 32 CA GLN B 31 C GLN B 31 O ALA B 32 CA ALA B 32 O DENSITY FOR THE SIDE CHAINS OF THE LISTED RESIDUES IS RELATIVELY POORLY DEFINED. THE MODEL REPRESENTS THE MOST PROBABLE CONFORMATIONS FOR THESE RESIDUES BASED ON THE OBSERVED DENSITY. LYS A 16 GLU A 27 LYS A 28 GLN A 31 ARG A 36 GLN A 139 GLU A 140 ARG A 198 GLU A 199 LYS A 213 LEU A 214 LYS A 215 LYS B 2 LEU B 13 LYS B 16 GLU B 20 GLU B 21 LYS B 28 ARG B 36 GLU B 140 ARG B 141 LYS B 173 ARG B 206 ASN B 211 LEU B 212 LYS B 213 LEU B 214 LYS B 215

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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)50,8614
Polymers50,7312
Non-polymers1312
Water1,56787
1
A: CARBONIC ANHYDRASE
B: CARBONIC ANHYDRASE
hetero molecules

A: CARBONIC ANHYDRASE
B: CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7238
Polymers101,4614
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Buried area15040 Å2
ΔGint-97 kcal/mol
Surface area33700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.244, 81.244, 162.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein CARBONIC ANHYDRASE


Mass: 25365.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YADF / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61517, 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.: 87 / 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: 2.64 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, PEG 400, MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mM1dropNaCl
41.6-1.8 Mammonium sulfate1reservoir
50.1 MMES1reservoir
64 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.96112,0.97950,0.97970,1.07812,1.28109
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 1999
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961121
20.97951
30.97971
41.078121
51.281091
ReflectionResolution: 2.13→45 Å / Num. all: 30857 / Num. obs: 237761 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 25.2
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.255 / Num. unique all: 4186 / % possible all: 94.5
Reflection
*PLUS
Num. obs: 30857 / Num. measured all: 237761

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→39.36 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2423088.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2848 10.1 %RANDOM
Rwork0.212 ---
obs0.212 28191 99.3 %-
all-30767 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.96 Å2 / ksol: 0.3548 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å20 Å20 Å2
2--4.85 Å20 Å2
3----9.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 2 87 3510
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 476 10.4 %
Rwork0.236 4083 -
obs-4559 98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor Rfree: 0.265 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.236

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