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- PDB-4wak: H. influenzae beta-carbonic anhydrase variant W39V/G41A -

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Basic information

Entry
Database: PDB / ID: 4wak
TitleH. influenzae beta-carbonic anhydrase variant W39V/G41A
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase allosteric site
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: 2.49 Å
AuthorsHoffmann, K.M. / Rowlett, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1157332 United States
CitationJournal: Biochemistry / Year: 2015
Title: Allosteric Reversion of Haemophilus influenzae beta-Carbonic Anhydrase via a Proline Shift.
Authors: Hoffmann, K.M. / Million-Perez, H.R. / Merkhofer, R. / Nicholson, H. / Rowlett, R.S.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,7207
Polymers52,4282
Non-polymers2925
Water1,820101
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)105,44014
Polymers104,8564
Non-polymers58410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area10480 Å2
ΔGint-42 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.330, 144.671, 129.010
Angle α, β, γ (deg.)90.00, 90, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase 2


Mass: 26213.932 Da / Num. of mol.: 2 / Mutation: W39V, G41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: can, HI_1301 / Plasmid: pTrc99a / 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 / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.02 % / Description: orthorhombic plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.15 M sodium potassium phosphate, 10 mg/mL protein

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Oct 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.49→29.5 Å / Num. obs: 16109 / % possible obs: 98.5 % / Redundancy: 9.6 % / Rsym value: 0.127 / Net I/σ(I): 15.1
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASERphasing
Cootmodel building
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A8D

2a8d


Resolution: 2.49→29.5 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.901 / SU B: 17.67 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25376 817 5.1 %RANDOM
Rwork0.18538 ---
obs0.18893 15291 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.294 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.64 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.49→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 11 101 2897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192864
X-RAY DIFFRACTIONr_bond_other_d0.0020.022782
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9323870
X-RAY DIFFRACTIONr_angle_other_deg0.8533.0016351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55723.664131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11615494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7041518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02686
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2252.5621405
X-RAY DIFFRACTIONr_mcbond_other2.2212.5611404
X-RAY DIFFRACTIONr_mcangle_it3.7893.8221748
X-RAY DIFFRACTIONr_mcangle_other3.7893.8231749
X-RAY DIFFRACTIONr_scbond_it2.5672.9331459
X-RAY DIFFRACTIONr_scbond_other2.5412.9271454
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3834.2542116
X-RAY DIFFRACTIONr_long_range_B_refined7.29220.4733313
X-RAY DIFFRACTIONr_long_range_B_other7.28520.4653291
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.489→2.553 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 61 -
Rwork0.265 1084 -
obs--96.06 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.17760.55460.19940.85590.6040.4738-0.06480.09880.1655-0.0570.08930.0385-0.03960.058-0.02450.0399-0.0384-0.00320.04040.02270.1856Chain A-2.90918.272-36.634
20.95020.067-0.32090.81690.24510.2737-0.0194-0.0933-0.02730.13310.01840.0949-0.00780.05750.0010.07990.03020.04210.1235-0.01320.0621Chain B-9.3652.819-13.877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 216
2X-RAY DIFFRACTION2B35 - 214

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