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- PDB-3e3f: H. influenzae beta-carbonic anhydrase, variant V47A with 100 mM b... -

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Basic information

Entry
Database: PDB / ID: 3e3f
TitleH. influenzae beta-carbonic anhydrase, variant V47A 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRowlett, R.S. / Mysliwiec, M.
CitationJournal: Biochemistry / Year: 2010
Title: Evidence for a bicarbonate "escort" site in Haemophilus influenzae beta-carbonic anhydrase .
Authors: Rowlett, R.S. / Hoffmann, K.M. / Failing, H. / Mysliwiec, M.M. / Samardzic, D.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _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)52,9549
Polymers52,5182
Non-polymers4367
Water1,51384
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)105,90818
Polymers105,0364
Non-polymers87214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11730 Å2
ΔGint-43 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.897, 83.897, 184.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 26258.932 Da / Num. of mol.: 2 / Mutation: V47A
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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CHO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 0.7 M sodium potassium tartrate, 100 mM sodium bicarbonate, 12 mg/mL protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→76.472 Å / Num. obs: 30001 / % possible obs: 99.2 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 22.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.1 / Num. measured all: 16260 / Num. unique all: 4077 / Rsym value: 0.367 / % possible all: 94.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A8D

2a8d


Resolution: 2.3→28.93 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.754 / SU B: 16.172 / SU ML: 0.186 / SU R Cruickshank DPI: 0.195 / SU Rfree: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1523 5.1 %RANDOM
Rwork0.193 ---
all0.195 29926 --
obs0.195 29926 99.13 %-
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: 86.61 Å2 / Biso mean: 48.922 Å2 / Biso min: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 22 84 3000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212973
X-RAY DIFFRACTIONr_bond_other_d0.0020.021950
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9344030
X-RAY DIFFRACTIONr_angle_other_deg0.94134754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8395363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.78523.869137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63915507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7291518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02597
X-RAY DIFFRACTIONr_nbd_refined0.230.2698
X-RAY DIFFRACTIONr_nbd_other0.1980.22004
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21440
X-RAY DIFFRACTIONr_nbtor_other0.0920.21613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2040.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.211
X-RAY DIFFRACTIONr_mcbond_it1.1321.52332
X-RAY DIFFRACTIONr_mcbond_other0.1841.5746
X-RAY DIFFRACTIONr_mcangle_it1.36322908
X-RAY DIFFRACTIONr_scbond_it2.19231334
X-RAY DIFFRACTIONr_scangle_it2.9834.51122
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 93 -
Rwork0.241 1890 -
all-1983 -
obs--90.84 %
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)
12.7987-0.49860.5152.24630.96393.74260.04680.28360.1103-0.4611-0.13440.1148-0.431-0.11530.0875-0.3680.0086-0.0705-0.5066-0.01840.3827-25.317-13.612-16.786
22.89630.3152-0.38063.32811.693.87620.0667-0.27050.2239-0.2415-0.11830.309-0.6163-0.10750.0516-0.39580.00070.0015-0.5792-0.07660.4173-27.148-2.516.993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA34 - 21534 - 215
2X-RAY DIFFRACTION2BB34 - 21634 - 216

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