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- PDB-1keq: Crystal Structure of F65A/Y131C Carbonic Anhydrase V, covalently ... -

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Entry
Database: PDB / ID: 1keq
TitleCrystal Structure of F65A/Y131C Carbonic Anhydrase V, covalently modified with 4-chloromethylimidazole
ComponentsF65A/Y131C-MI Carbonic Anhydrase V
KeywordsLYASE / PROTON TRANSFER / ENGINEERED RESIDUE
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / gluconeogenesis / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / mitochondrion / zinc ion binding / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / 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
4-METHYLIMIDAZOLE / ACETIC ACID / : / Carbonic anhydrase 5A, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsJude, K.M. / Wright, S.K. / Tu, C. / Silverman, D.N. / Viola, R.E. / Christianson, D.W.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystal structure of F65A/Y131C-methylimidazole carbonic anhydrase V reveals architectural features of an engineered proton shuttle.
Authors: Jude, K.M. / Wright, S.K. / Tu, C. / Silverman, D.N. / Viola, R.E. / Christianson, D.W.
#1: Journal: Arch.Biochem.Biophys. / Year: 1999
Title: Introduction of Histidine Analogs Leads to Enhanced Proton Transfer in Carbonic Anhydrase V
Authors: Earnhardt, J.N. / Wright, S.K. / Qian, M. / Tu, C. / Laipis, P.J. / Viola, R.E. / Silverman, D.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Structure determination of murine mitochondrial carbonic anhydrase V at 2.45-A resolution: implications for catalytic proton transfer and inhibitor design.
Authors: Boriack-Sjodin, P.A. / Heck, R.W. / Laipis, P.J. / Silverman, D.N. / Christianson, D.W.
History
DepositionNov 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 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

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Assembly

Deposited unit
A: F65A/Y131C-MI Carbonic Anhydrase V
B: F65A/Y131C-MI Carbonic Anhydrase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,04013
Polymers56,2792
Non-polymers76111
Water8,485471
1
A: F65A/Y131C-MI Carbonic Anhydrase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6118
Polymers28,1401
Non-polymers4717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F65A/Y131C-MI Carbonic Anhydrase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4295
Polymers28,1401
Non-polymers2904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.299, 66.703, 92.563
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein F65A/Y131C-MI Carbonic Anhydrase V


Mass: 28139.725 Da / Num. of mol.: 2 / Fragment: Carbonic Anhydrase Vc
Mutation: Truncation of mitochondrial leader sequence and first 21 residues, F65A/Y131C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MCA5C / Plasmid: PET31 T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P23589, carbonic anhydrase

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Non-polymers , 5 types, 482 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-4MZ / 4-METHYLIMIDAZOLE


Mass: 82.104 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6N2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.61 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 8000, sodium acetate, DTT, sucrose monolaurate, MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
21.2 mMsucrose monolaurate1drop
312 %PEG80001reservoir
4100 mMMES1reservoirpH6.7
5100 mMsodium acetate1reservoir
61 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2001 / Details: mirrors
RadiationMonochromator: Double-crystal, fixed-exit Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 46338 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3 / Num. unique all: 4557 / % possible all: 96.4
Reflection
*PLUS
Highest resolution: 1.88 Å / Lowest resolution: 25 Å / Num. obs: 46312 / % possible obs: 96.8 % / Num. measured all: 141410
Reflection shell
*PLUS
% possible obs: 87.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DMX

1dmx


Resolution: 1.88→24.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 253283.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: Examples of Stereochemistry target values (mmCIF item _refine.ndb_stereochemistry_target_values) Example 1: Engh & Huber
Details: Maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1808 4 %RANDOM
Rwork0.185 ---
obs0.185 45225 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0435 Å2 / ksol: 0.362292 e/Å3
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-1.16 Å2
2---3.52 Å20 Å2
3---3.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.88→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 31 481 4316
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 1.88→1.99 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 273 3.9 %
Rwork0.22 6651 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMMYTOPPAR:ACY.TOP
X-RAY DIFFRACTION3ION.PARAMMYTOPPAR:CMI.TOP
X-RAY DIFFRACTION4MYTOPPAR:ACY.PARAMWATER.TOP
X-RAY DIFFRACTION5MYTOPPAR:CMI.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 44468 / σ(F): 0 / % reflection Rfree: 4 % / Rfactor obs: 0.191 / Rfactor Rfree: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.234 / % reflection Rfree: 3.9 % / Rfactor Rwork: 0.22

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