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- PDB-2a8d: Haemophilus influenzae beta-carbonic anhydrase complexed with bic... -

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Basic information

Entry
Database: PDB / ID: 2a8d
TitleHaemophilus influenzae beta-carbonic anhydrase complexed with bicarbonate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / x-ray structure / carbonic anhydrase / protein-bicarbonate complex
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: 2.2 Å
AuthorsCronk, J.D. / Rowlett, R.S. / Zhang, K.Y.J. / Tu, C. / Endrizzi, J.A. / Lee, J. / Gareiss, P.C. / Preiss, J.R.
CitationJournal: Biochemistry / Year: 2006
Title: Identification of a Novel Noncatalytic Bicarbonate Binding Site in Eubacterial beta-Carbonic Anhydrase
Authors: Cronk, J.D. / Rowlett, R.S. / Zhang, K.Y.J. / Tu, C. / Endrizzi, J.A. / Lee, J. / Gareiss, P.C. / Preiss, J.R.
History
DepositionJul 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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)159,05724
Polymers157,7226
Non-polymers1,33518
Water5,729318
1
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)106,03816
Polymers105,1484
Non-polymers89012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-169 kcal/mol
Surface area32910 Å2
MethodPISA
2
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)106,03816
Polymers105,1484
Non-polymers89012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)232.807, 144.602, 52.101
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1279-

HOH

21A-1286-

HOH

31B-2251-

HOH

41B-2253-

HOH

51B-2265-

HOH

DetailsChains C, D, E, and F comprise a biological assembly. A second biological assembly can be formed from chains A and B by the operation -x, y, -z

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Components

#1: Protein
Carbonic anhydrase 2 / E.C.4.2.1.1 / beta-carbonic anhydrase


Mass: 26286.984 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: can / 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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG 400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 17, 2002
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 86683 / Num. obs: 86531 / % possible obs: 99.6 % / Observed criterion σ(I): 5 / Redundancy: 2.87 % / Biso Wilson estimate: 40.77 Å2 / Rsym value: 0.043 / Net I/σ(I): 22
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.29 % / Mean I/σ(I) obs: 3.18 / Num. unique all: 8444 / Rsym value: 0.262 / % possible all: 97.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I6P

1i6p


Resolution: 2.2→30 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 8684 -random
Rwork0.206 ---
all0.2061 86529 --
obs0.2061 86529 99.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.831 Å20 Å2-3.826 Å2
2---3.18 Å20 Å2
3----3.652 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10590 0 60 318 10968
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00562
X-RAY DIFFRACTIONc_angle_deg1.137
X-RAY DIFFRACTIONc_dihedral_angle_d20.75
X-RAY DIFFRACTIONc_improper_angle_d0.629
X-RAY DIFFRACTIONc_mcbond_it1.5151.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.1942
X-RAY DIFFRACTIONc_scangle_it3.3182.5
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.3459 820 -
Rwork0.2894 --
obs-8328 95.8 %

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