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- PDB-3e24: H. influenzae beta-carbonic anhydrase, variant W39F -

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Basic information

Entry
Database: PDB / ID: 3.0E+24
TitleH. influenzae beta-carbonic anhydrase, variant W39F
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
PHOSPHATE 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 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 1.3Aug 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0078
Polymers52,4962
Non-polymers5116
Water2,486138
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)106,01316
Polymers104,9924
Non-polymers1,02112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Buried area11960 Å2
ΔGint-121 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.173, 129.627, 144.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 26247.949 Da / Num. of mol.: 2 / Mutation: W39F
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 0.04 M ammonium dihydrogen phosphate, pH 4.3, 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: Nov 5, 2003
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 94242 / Rmerge(I) obs: 0.059 / Χ2: 1 / D res high: 2.3 Å / D res low: 30 Å / Num. obs: 20243 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.953097.210.0250.998
3.934.9599.610.0290.995
3.433.9399.510.0411.012
3.123.4399.310.0641.014
2.93.1299.210.0921.011
2.732.998.910.1281.012
2.592.7398.510.1761.005
2.482.5998.210.2171.015
2.382.489810.2580.987
2.32.3898.410.3140.995
ReflectionResolution: 2.301→29.37 Å / Num. all: 20243 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Redundancy: 4.6 % / Rsym value: 0.059 / Net I/σ(I): 22.24
Reflection shellResolution: 2.301→2.38 Å / Mean I/σ(I) obs: 4.52 / Rsym value: 0.316 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.448 / Cor.coef. Fo:Fc: 0.599
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A8D

2a8d


Resolution: 2.301→29.37 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0 / SU B: 11.197 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1990 9.8 %RANDOM
Rwork0.191 ---
all0.195 20243 --
obs0.195 20242 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: 103.42 Å2 / Biso mean: 44.069 Å2 / Biso min: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.301→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 22 138 3080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213006
X-RAY DIFFRACTIONr_bond_other_d0.0010.021981
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9394070
X-RAY DIFFRACTIONr_angle_other_deg0.9073.0024821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34824.043141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1715515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8371518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
X-RAY DIFFRACTIONr_nbd_refined0.2110.2703
X-RAY DIFFRACTIONr_nbd_other0.190.22065
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21450
X-RAY DIFFRACTIONr_nbtor_other0.0870.21481
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0510.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.219
X-RAY DIFFRACTIONr_mcbond_it0.941.52365
X-RAY DIFFRACTIONr_mcbond_other0.1061.5758
X-RAY DIFFRACTIONr_mcangle_it1.06722933
X-RAY DIFFRACTIONr_scbond_it1.36931364
X-RAY DIFFRACTIONr_scangle_it1.8634.51137
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 139 -
Rwork0.186 1305 -
all-1444 -
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)
11.4544-0.0586-0.27260.5969-0.39931.1751-0.03160.1736-0.122-0.11320.0044-0.02170.113-0.00830.0272-0.0167-0.00140.0203-0.0311-0.0254-0.038932.9960.86317.183
21.6454-0.4138-0.18351.2978-0.25951.07770.0144-0.00980.1285-0.00190.0203-0.0193-0.1643-0.0518-0.0346-0.00830.024-0.01-0.087-0.0006-0.023126.63883.48133.183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 220
2X-RAY DIFFRACTION2B35 - 216

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