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- PDB-1i6p: CRYSTAL STRUCTURE OF E. COLI BETA CARBONIC ANHYDRASE (ECCA) -

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Basic information

Entry
Database: PDB / ID: 1i6p
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


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 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
Revision 1.3Aug 9, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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. GLN A 31 CA ALA A 32 N ALA A 32 CA 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. GLU A 20 GLU A 21 LYS A 28 LEU A 29 GLN A 31 ALA A 32 GLN A 33 LYS A 34 GLU A 112 GLU A 140 ARG A 141 LYS A 169 LYS A 173 ARG A 189 ARG A 198 GLU A 199 LYS A 213 LEU A 214 LYS A 215

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1962
Polymers25,1311
Non-polymers651
Water1,11762
1
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)100,7858
Polymers100,5234
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation7_466y-1,x+1,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area15570 Å2
ΔGint-83 kcal/mol
Surface area33060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.535, 68.535, 85.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsA tetramer constructed from the operations -y, -x, -z; y, x, -z; -1-x, 1-y, z is thought to exist in solution under physiological conditions.

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Components

#1: Protein CARBONIC ANHYDRASE


Mass: 25130.779 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.009 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: ammonium sulfate, MES pH 6.3, 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
212 mg/mlprotein1drop
320 mMTris-HCl1drop
4100 mM1dropNaCl
51.6-1.8 Mammonium sulfate1reservoir
60.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 8, 1999 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 90500 / Num. obs: 13974 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 4.4 / % possible all: 96.9

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I6O

1i6o


Resolution: 2→42.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 334555.69 / 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
Rfree0.202 1379 10.1 %RANDOM
Rwork0.176 ---
obs0.176 13653 94.7 %-
all-13958 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.43 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 1 62 1778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 223 10.2 %
Rwork0.191 1955 -
obs--92.6 %
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: 28.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62
LS refinement shell
*PLUS
Rfactor Rfree: 0.215 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.191

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