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- PDB-4xz5: Structure of the thermostable alpha-Carbonic Anydrase from Thiomi... -

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Basic information

Entry
Database: PDB / ID: 4xz5
TitleStructure of the thermostable alpha-Carbonic Anydrase from Thiomicrospira crunogena XCL-2 gammaproteobacterium
ComponentsCarbonic anhydrase, alpha family
KeywordsLYASE / Carbonic Anhydrase / Thiomicrospira crunogena XCL-2 / thermostability / CO2 sequestration
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / Carbonic anhydrase, alpha family
Similarity search - Component
Biological speciesThiomicrospira crunogena
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.596 Å
AuthorsMahon, B.P. / Diaz-Torres, N.A. / Pinard, M.A. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM25154 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and biophysical characterization of the alpha-carbonic anhydrase from the gammaproteobacterium Thiomicrospira crunogena XCL-2: insights into engineering thermostable enzymes for CO2 sequestration.
Authors: Diaz-Torres, N.A. / Mahon, B.P. / Boone, C.D. / Pinard, M.A. / Tu, C. / Ng, R. / Agbandje-McKenna, M. / Silverman, D. / Scott, K. / McKenna, R.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Aug 9, 2017Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase, alpha family
B: Carbonic anhydrase, alpha family
C: Carbonic anhydrase, alpha family
D: Carbonic anhydrase, alpha family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,24312
Polymers106,7374
Non-polymers5068
Water66737
1
A: Carbonic anhydrase, alpha family
B: Carbonic anhydrase, alpha family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6216
Polymers53,3682
Non-polymers2534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-86 kcal/mol
Surface area20340 Å2
MethodPISA
2
C: Carbonic anhydrase, alpha family
D: Carbonic anhydrase, alpha family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6216
Polymers53,3682
Non-polymers2534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-84 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.059, 102.228, 105.021
Angle α, β, γ (deg.)90.000, 127.260, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 75 - 304 / Label seq-ID: 1 - 230

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
Carbonic anhydrase, alpha family


Mass: 26684.229 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiomicrospira crunogena (strain XCL-2) (bacteria)
Strain: XCL-2 / Gene: Tcr_1545 / Production host: Escherichia coli (E. coli) / References: UniProt: Q31FD6, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate trihydrate pH 4.6, 16% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9177 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 32793 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.87 Å2 / Rmerge(I) obs: 0.1 / Χ2: 0.815 / Net I/av σ(I): 9.212 / Net I/σ(I): 9.4 / Num. measured all: 120808
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.693.50.40532530.88199.1
2.69-2.83.60.31832570.83899.4
2.8-2.933.60.24532330.87499.7
2.93-3.083.70.20532800.93699.9
3.08-3.273.70.14333030.92100
3.27-3.523.80.10532590.834100
3.52-3.883.80.0832810.768100
3.88-4.433.80.06332740.675100
4.43-5.573.80.05232960.777100
5.57-203.70.0733570.666100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
ADSCdata collection
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 2.596→19.912 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1643 5.01 %Random Selection
Rwork0.1713 31139 --
obs0.1747 32782 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.97 Å2 / Biso mean: 35.0159 Å2 / Biso min: 4.14 Å2
Refinement stepCycle: final / Resolution: 2.596→19.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7440 0 20 37 7497
Biso mean--29.02 24.26 -
Num. residues----920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097692
X-RAY DIFFRACTIONf_angle_d1.30310436
X-RAY DIFFRACTIONf_chiral_restr0.0561072
X-RAY DIFFRACTIONf_plane_restr0.0081352
X-RAY DIFFRACTIONf_dihedral_angle_d14.9362852
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4533X-RAY DIFFRACTION9.444TORSIONAL
12B4533X-RAY DIFFRACTION9.444TORSIONAL
13C4533X-RAY DIFFRACTION9.444TORSIONAL
14D4533X-RAY DIFFRACTION9.444TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5964-2.67260.30581270.21462409253692
2.6726-2.75860.33791350.22722578271399
2.7586-2.8570.31621370.205525802717100
2.857-2.9710.2821390.202826162755100
2.971-3.10570.27431400.204226052745100
3.1057-3.26880.28051350.194726302765100
3.2688-3.47260.28161350.1825632698100
3.4726-3.73910.21111380.16726372775100
3.7391-4.11240.22581370.154526062743100
4.1124-4.70060.1931380.135426222760100
4.7006-5.89660.1881420.139626172759100
5.8966-19.91280.20661400.16526762816100
Refinement TLS params.Method: refined / Origin x: -21.3263 Å / Origin y: -21.5212 Å / Origin z: 189.9641 Å
111213212223313233
T0.0439 Å2-0.0241 Å20.0006 Å2-0.0468 Å2-0.0247 Å2--0.0396 Å2
L0.0584 °20.003 °2-0.0115 °2-0.0343 °20.0022 °2--0.0372 °2
S0.051 Å °0.0325 Å °-0.0399 Å °0.002 Å °-0.0235 Å °-0.05 Å °-0.0126 Å °-0.0542 Å °0.0341 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA75 - 304
2X-RAY DIFFRACTION1allE262 - 265
3X-RAY DIFFRACTION1allB75 - 304
4X-RAY DIFFRACTION1allC75 - 304
5X-RAY DIFFRACTION1allD75 - 304
6X-RAY DIFFRACTION1allF5 - 76
7X-RAY DIFFRACTION1allG303 - 306

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