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- PDB-3e2w: H. influenzae beta-carbonic anhydrase, variant Y181F with 1M bica... -

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Basic information

Entry
Database: PDB / ID: 3e2w
TitleH. influenzae beta-carbonic anhydrase, variant Y181F with 1M 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 / Resolution: 2.296 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 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 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 / Item: _software.name
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
Water4,630257
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 area17800 Å2
ΔGint-253 kcal/mol
Surface area34440 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 area18050 Å2
ΔGint-246 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.141, 145.225, 53.499
Angle α, β, γ (deg.)90.000, 93.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-261-

HOH

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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.: 257 / 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: 3.08 Å3/Da / Density % sol: 60.01 %
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, crystals soaked in this solution plus 30% glycerol and 1 M sodium bicarbonate, 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 21, 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: 2.296→26.2 Å / Num. obs: 77677 / % possible obs: 99.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.061 / Χ2: 1.004 / Net I/σ(I): 13.78
Reflection shellResolution: 2.296→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.73 / Num. unique all: 7731 / Χ2: 0.987 / % possible all: 99.2

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Processing

Software
NameVersionClassification
EPMRphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A8D

2a8d


Resolution: 2.296→26.2 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.464 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3911 5 %RANDOM
Rwork0.205 ---
all0.207 77675 --
obs0.207 77675 91.47 %-
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: 127.91 Å2 / Biso mean: 67.431 Å2 / Biso min: 39.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.17 Å2
2--0.06 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.296→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9750 0 70 257 10077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02110034
X-RAY DIFFRACTIONr_bond_other_d0.0010.026655
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.93213569
X-RAY DIFFRACTIONr_angle_other_deg0.9623.00116182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54851205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36424.113479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.192151749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3021560
X-RAY DIFFRACTIONr_chiral_restr0.0730.21503
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022027
X-RAY DIFFRACTIONr_nbd_refined0.1990.21812
X-RAY DIFFRACTIONr_nbd_other0.1760.25886
X-RAY DIFFRACTIONr_nbtor_refined0.1640.24491
X-RAY DIFFRACTIONr_nbtor_other0.0840.24637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.216
X-RAY DIFFRACTIONr_mcbond_it0.6271.57871
X-RAY DIFFRACTIONr_mcbond_other0.091.52485
X-RAY DIFFRACTIONr_mcangle_it0.76529688
X-RAY DIFFRACTIONr_scbond_it1.22734707
X-RAY DIFFRACTIONr_scangle_it1.764.53881
LS refinement shellResolution: 2.296→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 89 -
Rwork0.221 2066 -
all-2155 -
obs--34.64 %
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)
12.4336-0.09940.91221.3-0.32181.09590.14580.1474-0.50980.0123-0.044-0.06960.20240.1513-0.1018-0.10370.0686-0.0736-0.1894-0.0247-0.22628.58251.38828.35
22.72340.3406-0.0581.9387-0.32452.967-0.11690.1050.47940.0034-0.0097-0.0825-0.8620.31280.12660.0954-0.1228-0.1229-0.20260.054-0.26587.99985.52523.412
31.6377-0.19190.47373.2574-0.6443.1446-0.0198-0.04240.163-0.01310.05540.4237-0.524-0.5791-0.03560.03010.0742-0.0595-0.1820.0016-0.362150.367121.8454.543
42.76810.01190.62.33580.10371.667-0.04420.1454-0.0685-0.06910.0047-0.68080.07920.30310.0396-0.0921-0.0607-0.0292-0.19940.0166-0.227583.942106.8788.37
52.3020.3383-0.3032.612-0.25382.96950.0210.01380.09180.00420.06930.6388-0.0661-0.8263-0.0903-0.0851-0.0328-0.0428-0.0320.0289-0.285842.429105.78410.799
61.50380.11690.17182.77110.34941.19780.05230.0988-0.2671-0.0770.0269-0.44110.32280.1657-0.07920.05820.002-0.0346-0.2638-0.0108-0.327575.48790.8824.145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION2B1 - 217
3X-RAY DIFFRACTION3C1 - 216
4X-RAY DIFFRACTION4D1 - 214
5X-RAY DIFFRACTION5E1 - 216
6X-RAY DIFFRACTION6F1 - 214

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