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- PDB-3e1v: H. influenzae beta-carbonic anhydrase, variant D44N -

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Basic information

Entry
Database: PDB / ID: 3e1v
TitleH. influenzae beta-carbonic anhydrase, variant D44N
ComponentsCarbonic anhydrase 2
KeywordsLYASE / beta carbonic anhydrase / active 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsRowlett, R.S. / Chapnick, D.A. / Shah, S.
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 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 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 / 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)52,7034
Polymers52,5722
Non-polymers1312
Water37821
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)105,4068
Polymers105,1444
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area9810 Å2
ΔGint-58 kcal/mol
Surface area27850 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.574, 81.574, 187.846
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 / Carbonate dehydratase 2


Mass: 26286.000 Da / Num. of mol.: 2 / Mutation: D44N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 0.8 M sodium acetate, pH 6.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jan 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→74.824 Å / Num. all: 162075 / Num. obs: 16060 / % possible obs: 98.5 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 19.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.9560.3412.31343722490.34197.4
2.95-3.136.30.2543.11352121600.25498.1
3.13-3.346.30.184.31271320330.1898.3
3.34-3.616.30.1236.11201219160.12398.6
3.61-3.966.30.0898.21114017770.08998.8
3.96-4.426.20.06910.11009416220.06998.9
4.42-5.1120.90.0848.73036214520.08499.4
5.11-6.26230.1067.12890912580.10699.6
6.26-8.85210.0710.52118610070.0799.9
8.85-29.2314.80.03120.487015860.03197

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å29.22 Å
Translation2.8 Å29.22 Å

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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: 2.8→28.84 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.866 / SU B: 22.129 / SU ML: 0.209 / SU R Cruickshank DPI: 0.505 / SU Rfree: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 812 5.1 %RANDOM
Rwork0.194 ---
obs0.196 16044 98.13 %-
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: 71.51 Å2 / Biso mean: 39.558 Å2 / Biso min: 7.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 2 21 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212960
X-RAY DIFFRACTIONr_bond_other_d0.0010.021954
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.934014
X-RAY DIFFRACTIONr_angle_other_deg0.8753.0024758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1865362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.51623.824136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22815508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9821518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
X-RAY DIFFRACTIONr_nbd_refined0.2320.2775
X-RAY DIFFRACTIONr_nbd_other0.2040.22115
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21436
X-RAY DIFFRACTIONr_nbtor_other0.0910.21583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.24
X-RAY DIFFRACTIONr_mcbond_it0.7141.52326
X-RAY DIFFRACTIONr_mcbond_other0.0821.5744
X-RAY DIFFRACTIONr_mcangle_it0.84322904
X-RAY DIFFRACTIONr_scbond_it1.06231340
X-RAY DIFFRACTIONr_scangle_it1.6774.51110
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 70 -
Rwork0.244 1043 -
all-1113 -
obs--96.45 %
Refinement TLS params.

S11: 0.0749 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)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)
13.04110.1905-0.71113.2294-1.09813.45040.38210.0167-0.3922-0.1149-0.10570.32830.05120.04-0.1555-0.01340.0326-0.19740.0357-0.017965.69553.965171.04
22.77020.25610.26483.7708-0.78483.6716-0.0962-0.21530.0955-0.0139-0.38270.5730.3579-0.061-0.05960.0091-0.006-0.2840.04510.072168.04643.202194.621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA34 - 21534 - 215
2X-RAY DIFFRACTION2BB34 - 21534 - 215

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