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- PDB-3e2a: H. influenzae beta-carbonic anhydrase, variant Y181F with 100 mM ... -

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Basic information

Entry
Database: PDB / ID: 3e2a
TitleH. influenzae beta-carbonic anhydrase, variant Y181F with 100 mM bicarbonate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / beta carbonic anhydrase / allosteric site mutant / Metal-binding
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
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
BICARBONATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.301 Å
AuthorsRowlett, R.S. / Lee, J.
CitationJournal: Biochemistry / Year: 2009
Title: Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase.
Authors: Rowlett, R.S. / Tu, C. / Lee, J. / Herman, A.G. / Chapnick, D.A. / Shah, S.H. / Gareiss, P.C.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
C: Carbonic anhydrase 2
D: Carbonic anhydrase 2
E: Carbonic anhydrase 2
F: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,23225
Polymers157,6266
Non-polymers1,60619
Water2,846158
1
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,11416
Polymers105,0844
Non-polymers1,03012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17730 Å2
ΔGint-257 kcal/mol
Surface area31510 Å2
MethodPISA
2
C: Carbonic anhydrase 2
D: Carbonic anhydrase 2
E: Carbonic anhydrase 2
F: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,17517
Polymers105,0844
Non-polymers1,09113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18010 Å2
ΔGint-256 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.606, 145.512, 53.234
Angle α, β, γ (deg.)90.000, 93.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Carbonic anhydrase 2 / E.C.4.2.1.1 / Carbonate dehydratase 2


Mass: 26270.984 Da / Num. of mol.: 6 / Mutation: Y181F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: can, HI1301 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P45148, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 1.5 M ammonium sulfate, 4% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 13, 2003
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.301→25 Å / Num. obs: 77406 / % possible obs: 100 % / Redundancy: 3.53 % / Rmerge(I) obs: 0.065 / Χ2: 0.999 / Net I/σ(I): 18.8
Reflection shellResolution: 2.301→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.6 / Num. unique all: 7649 / Χ2: 0.989 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A8D

2a8d


Resolution: 2.301→24.78 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.15 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 7808 10.1 %RANDOM
Rwork0.201 ---
all0.205 77404 --
obs0.205 77404 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.25 Å2 / Biso mean: 44.228 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.301→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9906 0 70 158 10134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02110192
X-RAY DIFFRACTIONr_bond_other_d0.0010.026746
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.93213784
X-RAY DIFFRACTIONr_angle_other_deg0.8863.00116408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92151224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52724.204490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.031151777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4811560
X-RAY DIFFRACTIONr_chiral_restr0.0730.21529
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022050
X-RAY DIFFRACTIONr_nbd_refined0.220.22230
X-RAY DIFFRACTIONr_nbd_other0.1890.26722
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24879
X-RAY DIFFRACTIONr_nbtor_other0.0880.24998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2325
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0630.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1640.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3410.215
X-RAY DIFFRACTIONr_mcbond_it0.7511.57980
X-RAY DIFFRACTIONr_mcbond_other0.111.52525
X-RAY DIFFRACTIONr_mcangle_it0.92129840
X-RAY DIFFRACTIONr_scbond_it1.48134745
X-RAY DIFFRACTIONr_scangle_it2.0474.53944
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 582 -
Rwork0.215 4982 -
all-5564 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1854-0.06860.96880.7589-0.20180.94060.22060.2303-0.4950.0574-0.0119-0.10960.20110.1866-0.2087-0.18530.0755-0.0468-0.0865-0.06530.08279.30552.71427.651
22.2628-0.02540.32461.8893-0.47133.0816-0.19570.2140.30820.01930.0059-0.226-0.85180.48070.1898-0.0585-0.1418-0.032-0.09970.05-0.03588.84784.14923.628
31.4747-0.41970.39782.5835-0.69972.6425-0.0356-0.01750.1483-0.01030.02880.2043-0.5454-0.3760.0067-0.06620.06070.0262-0.1339-0.0024-0.096848.303122.9454.679
41.915-0.0440.49871.61780.10881.386-0.05010.11010.0778-0.0195-0.0279-0.4899-0.01780.23190.0781-0.1733-0.06290.0424-0.10020.02060.026776.676109.1297.767
51.56290.0694-0.37412.2361-0.56552.23110.0139-0.0203-0.08680.02540.07630.51030.0268-0.6919-0.0902-0.2113-0.04380.02830.03150.0074-0.017239.539103.84910.329
61.36750.3030.07362.05750.29530.96680.05140.017-0.2076-0.0413-0.0336-0.24850.29330.0624-0.0178-0.06660.00030.0378-0.1719-0.0008-0.055667.74890.2114.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 221
2X-RAY DIFFRACTION2B1 - 221
3X-RAY DIFFRACTION3C1 - 219
4X-RAY DIFFRACTION4D1 - 215
5X-RAY DIFFRACTION5E1 - 220
6X-RAY DIFFRACTION6F1 - 219

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