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- PDB-4waj: H. influenzae beta-carbonic anhydase variant P48S/A49P -

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Basic information

Entry
Database: PDB / ID: 4waj
TitleH. influenzae beta-carbonic anhydase variant P48S/A49P
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase allosteric reversion
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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRowlett, R.S. / Hoffmann, 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 13, 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 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1218
Polymers52,6062
Non-polymers5156
Water1,27971
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)106,24216
Polymers105,2124
Non-polymers1,03012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area15690 Å2
ΔGint-220 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.777, 82.777, 186.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 26302.984 Da / Num. of mol.: 2 / Mutation: 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 / Details (production host): 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.05 Å3/Da / Density % sol: 59.64 % / Description: tetragonal
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.5 M ammonium sulfate, 5% DMSO, 0.1 M MES

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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: Aug 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→75.66 Å / Num. obs: 18148 / % possible obs: 97.9 % / Redundancy: 5.9 % / Net I/σ(I): 19.3
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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Processing

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

2a8d


Resolution: 2.7→75.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.921 / SU B: 19.516 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23197 931 5.1 %RANDOM
Rwork0.16068 ---
obs0.16414 17217 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.187 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å2-0 Å2
2--1.65 Å2-0 Å2
3----3.29 Å2
Refinement stepCycle: 1 / Resolution: 2.7→75.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 22 71 3296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193311
X-RAY DIFFRACTIONr_bond_other_d0.0020.023155
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9354487
X-RAY DIFFRACTIONr_angle_other_deg0.8563.0017224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2624.214159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12515575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.431519
X-RAY DIFFRACTIONr_chiral_restr0.0810.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
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_it2.5543.0521602
X-RAY DIFFRACTIONr_mcbond_other2.5553.0491601
X-RAY DIFFRACTIONr_mcangle_it4.2474.5642000
X-RAY DIFFRACTIONr_mcangle_other4.2464.5672001
X-RAY DIFFRACTIONr_scbond_it3.1543.5141708
X-RAY DIFFRACTIONr_scbond_other3.0263.4931693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.035.0592462
X-RAY DIFFRACTIONr_long_range_B_refined7.1924.4413830
X-RAY DIFFRACTIONr_long_range_B_other7.15724.4153806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 71 -
Rwork0.257 1177 -
obs--92.38 %
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)
10.62130.18570.49690.387-0.35031.4508-0.04340.01030.0986-0.05220.0123-0.01850.0305-0.24060.03110.04450.0002-0.0430.20570.04410.1627Chain A-39.247-13.914-6.763
20.6901-0.2818-0.26330.3899-0.48051.36560.0060.18780.0383-0.0653-0.0941-0.06340.1612-0.02850.08810.1122-0.02810.03090.12790.00360.1334Chain B-14.131-31.515-14.842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 216
2X-RAY DIFFRACTION2B1 - 215

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