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- PDB-3mf3: Cobalt(II)-Substituted Haemophilus influenzae B-Carbonic Anhydrase -

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Basic information

Entry
Database: PDB / ID: 3mf3
TitleCobalt(II)-Substituted Haemophilus influenzae B-Carbonic Anhydrase
ComponentsCarbonic anhydrase 2
KeywordsLYASE / beta-carbonic anhydrase / Haemophilus influenzae / bicarbonate / zinc metalloenzyme / cobalt substitution
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
ACETATE ION / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHoffmann, K.M. / Rowlett, R.S.
CitationJournal: To be Published
Title: The Structure and Properties of Cobalt(II)-Substituted Haemophilus influenzae B-Carbonic Anhydrase.
Authors: Hoffmann, K.M. / Samardzic, D. / van den Heever, K. / Rowlett, R.S.
History
DepositionApr 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2019Group: Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Carbonic anhydrase 2
D: Carbonic anhydrase 2
E: Carbonic anhydrase 2
F: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,49716
Polymers151,9076
Non-polymers59010
Water3,675204
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)101,74412
Polymers101,2724
Non-polymers4728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16510 Å2
ΔGint-90 kcal/mol
Surface area33830 Å2
MethodPISA
2
C: Carbonic anhydrase 2
D: Carbonic anhydrase 2
E: Carbonic anhydrase 2
F: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,62510
Polymers101,2724
Non-polymers3546
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18000 Å2
ΔGint-165 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.492, 144.929, 52.215
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-256-

HOH

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Components

#1: Protein
Carbonic anhydrase 2 / Carbonate dehydratase 2


Mass: 25317.910 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: can, HI1301 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P45148, carbonic anhydrase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate, 0.1 M Tris-Cl, 0.1 M ammonium sulfate, 27% PEG 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 21, 2008 / Details: collimating mirror
RadiationMonochromator: collimating mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.5→122.463 Å / Num. all: 58139 / Num. obs: 58139 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 4.1 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.421 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
DPS(CHESS)data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A8C

2a8c


Resolution: 2.5→29.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.373 / SU ML: 0.189 / SU R Cruickshank DPI: 0.469 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22805 2941 5.1 %RANDOM
Rwork0.17304 ---
obs0.17584 55195 98.91 %-
all-58139 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.11 Å2
2--0.12 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10483 0 22 204 10709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02110729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.92714532
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29351298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20124.286525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.207151877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5311560
X-RAY DIFFRACTIONr_chiral_restr0.1080.21608
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028088
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9491.56472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.818210408
X-RAY DIFFRACTIONr_scbond_it2.72134257
X-RAY DIFFRACTIONr_scangle_it4.3634.54124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 224 -
Rwork0.223 4002 -
obs--98.65 %
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)
11.6489-0.08370.51910.7168-0.38130.50370.0241-0.0105-0.31310.0098-0.0623-0.12290.05090.09530.03820.02010.0319-0.00490.1920.04120.19797.745-92.38427.857
21.3812-0.1415-0.27030.6639-0.08430.5680.00190.06140.22470.0395-0.1165-0.1423-0.27550.12540.11460.1488-0.0788-0.08880.17660.06740.14257.202-58.55922.878
30.94350.09540.18631.9063-0.67141.1120.0176-0.01920.182-0.08010.1040.2123-0.2068-0.2311-0.12170.1790.0131-0.00310.07010.04740.093846.44-22.2834.149
41.3730.06980.24551.72540.0630.49650.0428-0.0499-0.0569-0.10490.0086-0.50580.04360.2069-0.05150.1008-0.04090.01860.1423-0.00180.20377.041-36.8847.941
51.00930.2412-0.05372.052-0.36830.94360.0346-0.0864-0.0891-0.0020.17880.4437-0.0346-0.3151-0.21340.1062-0.0777-0.00530.18950.10310.13939.102-38.1610.566
61.00710.46650.00881.66520.39670.67280.0461-0.0413-0.2348-0.19810.0935-0.24580.30780.1235-0.13960.31260.0279-0.00340.0302-0.03420.151169.218-52.8683.843
70.80890.6343-0.29310.5626-0.19930.15610.0647-0.071-0.0658-0.0007-0.0648-0.0609-0.05-0.02720.00010.1371-0.0174-0.05330.08550.06790.094738.248-53.42714.839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 221
2X-RAY DIFFRACTION2B1 - 221
3X-RAY DIFFRACTION3C1 - 217
4X-RAY DIFFRACTION4D2 - 215
5X-RAY DIFFRACTION5E2 - 216
6X-RAY DIFFRACTION6F1 - 217
7X-RAY DIFFRACTION7A231 - 235
8X-RAY DIFFRACTION7C231 - 245
9X-RAY DIFFRACTION7B231 - 242
10X-RAY DIFFRACTION7E231 - 236
11X-RAY DIFFRACTION7D231 - 237
12X-RAY DIFFRACTION7F231 - 237

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