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- PDB-1ym3: Crystal Structure of carbonic anhydrase RV3588c from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 1ym3
TitleCrystal Structure of carbonic anhydrase RV3588c from Mycobacterium tuberculosis
ComponentsCARBONIC ANHYDRASE (CARBONATE DEHYDRATASE) (CARBONIC DEHYDRATASE)
KeywordsLYASE / Zn protein / Structural Proteomics in Europe / SPINE / Structural Genomics
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 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCovarrubias, A.S. / Larsson, A.M. / Hogbom, M. / Lindberg, J. / Bergfors, T. / Bjorkelid, C. / Mowbray, S.L. / Unge, T. / Jones, T.A. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and function of carbonic anhydrases from Mycobacterium tuberculosis.
Authors: Suarez Covarrubias, A. / Larsson, A.M. / Hogbom, M. / Lindberg, J. / Bergfors, T. / Bjorkelid, C. / Mowbray, S.L. / Unge, T. / Jones, T.A.
History
DepositionJan 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 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_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_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.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.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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE (CARBONATE DEHYDRATASE) (CARBONIC DEHYDRATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8633
Polymers22,7741
Non-polymers902
Water2,342130
1
A: CARBONIC ANHYDRASE (CARBONATE DEHYDRATASE) (CARBONIC DEHYDRATASE)
hetero molecules

A: CARBONIC ANHYDRASE (CARBONATE DEHYDRATASE) (CARBONIC DEHYDRATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7276
Polymers45,5472
Non-polymers1794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3500 Å2
ΔGint-37 kcal/mol
Surface area15730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.377, 56.377, 104.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -Y, -X, 1/2-Z

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Components

#1: Protein CARBONIC ANHYDRASE (CARBONATE DEHYDRATASE) (CARBONIC DEHYDRATASE)


Mass: 22773.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3588c / Plasmid: pCRT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: O53573, UniProt: P9WPJ9*PLUS, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.9 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MgCl2, PEG 400, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.085 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 2, 2004 / Details: Vertically focusing cylindrical mirror
RadiationMonochromator: Single asymmetrically cut Si(111) crystal with horizontal diffraction plane. The crystal is bendable for horizontal focusing.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.085 Å / Relative weight: 1
ReflectionResolution: 1.75→26.2 Å / Num. all: 13934 / Num. obs: 13934 / % possible obs: 83.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.044 / Net I/σ(I): 23.35
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.298 / % possible all: 80.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I6O and 1DDZ

1i6o

1ddz


Resolution: 1.75→26.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.595 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22946 734 5 %RANDOM
Rwork0.17876 ---
all0.18134 13934 --
obs0.18134 13934 82.92 %-
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: 23.207 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 0 2 130 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211468
X-RAY DIFFRACTIONr_bond_other_d0.0020.021385
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9461994
X-RAY DIFFRACTIONr_angle_other_deg0.87433186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5565193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021678
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02300
X-RAY DIFFRACTIONr_nbd_refined0.2080.2288
X-RAY DIFFRACTIONr_nbd_other0.2290.21551
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.2828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6190.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.981.5956
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75321532
X-RAY DIFFRACTIONr_scbond_it2.6823512
X-RAY DIFFRACTIONr_scangle_it4.2724.5462
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.748→1.794 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 59
Rwork0.186 956
Refinement TLS params.Method: refined / Origin x: 20.0998 Å / Origin y: 22.5969 Å / Origin z: 21.0858 Å
111213212223313233
T0.0381 Å2-0.0001 Å2-0.0093 Å2-0.0095 Å2-0.0022 Å2--0.0326 Å2
L0.5139 °20.1853 °20.175 °2-0.8383 °20.3555 °2--0.9139 °2
S0.0211 Å °-0.0526 Å °-0.0233 Å °-0.0872 Å °-0.0219 Å °0.0198 Å °0.0856 Å °-0.0211 Å °0.0009 Å °

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