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- PDB-4wam: H. influenzae beta-carbonic anhydrase variant W39V/G41A/P48S/A49P -

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Basic information

Entry
Database: PDB / ID: 4wam
TitleH. influenzae beta-carbonic anhydrase variant W39V/G41A/P48S/A49P
Componentsbeta-carbonic anhydrase
KeywordsLYASE / beta-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
PHOSPHATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsRowlett, R.S. / Hoffman, K.M.
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 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
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 / struct_keywords
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 / _struct_keywords.text
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-carbonic anhydrase
B: beta-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9718
Polymers52,4602
Non-polymers5116
Water2,594144
1
A: beta-carbonic anhydrase
B: beta-carbonic anhydrase
hetero molecules

A: beta-carbonic anhydrase
B: beta-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,94116
Polymers104,9204
Non-polymers1,02112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Buried area11970 Å2
ΔGint-116 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.162, 130.259, 143.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-418-

HOH

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Components

#1: Protein beta-carbonic anhydrase / Carbonate dehydratase 2


Mass: 26229.932 Da / Num. of mol.: 2 / Mutation: W39V, G41A, P48S, A49P
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-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 144 / 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: 0.30 M sodium potassium phosphate, 12 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: May 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→96.56 Å / Num. obs: 22403 / % possible obs: 95.3 % / Redundancy: 3.3 % / Rsym value: 0.101 / Net I/σ(I): 7.2
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 1.7 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASERphasing
Cootmodel building
SCALAdata scaling
RefinementResolution: 2.2→96.56 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.846 / SU B: 12.834 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28681 1163 5.2 %RANDOM
Rwork0.23224 ---
obs0.23508 21239 95.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.127 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.2→96.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 22 144 3001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192924
X-RAY DIFFRACTIONr_bond_other_d0.0020.022834
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9413955
X-RAY DIFFRACTIONr_angle_other_deg0.9183.0016477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83923.712132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17415506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5061518
X-RAY DIFFRACTIONr_chiral_restr0.1060.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
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_it1.6311.7351428
X-RAY DIFFRACTIONr_mcbond_other1.6311.7321427
X-RAY DIFFRACTIONr_mcangle_it2.7442.5741775
X-RAY DIFFRACTIONr_mcangle_other2.7432.5771776
X-RAY DIFFRACTIONr_scbond_it1.9892.0381496
X-RAY DIFFRACTIONr_scbond_other1.8862.0171478
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2072.9332155
X-RAY DIFFRACTIONr_long_range_B_refined6.08114.3713417
X-RAY DIFFRACTIONr_long_range_B_other5.86914.2193369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.663 57 -
Rwork0.628 1173 -
obs--72.74 %
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)
11.3453-0.27580.22080.66650.18050.70420.01070.22230.1255-0.0862-0.00410.0072-0.0096-0.0065-0.00660.02940.0057-0.00950.12230.02230.0174-8.8213.31917.499
21.4342-0.3170.18560.7202-0.07580.6515-0.0018-0.0004-0.2002-0.04210.00560.02620.08310.029-0.00380.01720.01470.0030.0338-0.00390.0415-2.808-18.63632.813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 221
2X-RAY DIFFRACTION2B34 - 217

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