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- PDB-1ylk: Crystal Structure of Rv1284 from Mycobacterium tuberculosis in Co... -

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Basic information

Entry
Database: PDB / ID: 1ylk
TitleCrystal Structure of Rv1284 from Mycobacterium tuberculosis in Complex with Thiocyanate
ComponentsHypothetical protein Rv1284/MT1322Hypothesis
KeywordsUNKNOWN FUNCTION / Rv1284 / homodimer / alpha/beta-fold / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding / plasma membrane
Similarity search - Function
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
THIOCYANATE ION / Beta-carbonic anhydrase 1 / Beta-carbonic anhydrase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 19, 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: Source and taxonomy / 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_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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein Rv1284/MT1322
B: Hypothetical protein Rv1284/MT1322
C: Hypothetical protein Rv1284/MT1322
D: Hypothetical protein Rv1284/MT1322
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,57513
Polymers77,0234
Non-polymers5529
Water4,828268
1
A: Hypothetical protein Rv1284/MT1322
B: Hypothetical protein Rv1284/MT1322
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8177
Polymers38,5122
Non-polymers3055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-131 kcal/mol
Surface area12970 Å2
MethodPISA
2
C: Hypothetical protein Rv1284/MT1322
D: Hypothetical protein Rv1284/MT1322
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7596
Polymers38,5122
Non-polymers2474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-128 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.164, 154.074, 156.943
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11D-444-

HOH

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Components

#1: Protein
Hypothetical protein Rv1284/MT1322 / Hypothesis


Mass: 19255.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1284 / Plasmid: pCRT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P64797, UniProt: P9WPJ7*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium thiocyanate, polyethylene glycol 2000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2003 / Details: Sagitally focusing Ge(220) and a multilayer
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→44.3 Å / Num. obs: 38625 / % possible obs: 94.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 26.923 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.079 / Net I/σ(I): 20.3
Reflection shellResolution: 2→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1363 / Rsym value: 0.399 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G5C

1g5c


Resolution: 2→42.26 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.709 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22645 1946 5 %RANDOM
Rwork0.18082 ---
all0.18314 ---
obs0.18314 36658 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 19 268 5371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225194
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9637049
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24423.22236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27915868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6341548
X-RAY DIFFRACTIONr_chiral_restr0.0840.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023928
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.22502
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23587
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2369
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.030.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5231.53258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96525297
X-RAY DIFFRACTIONr_scbond_it1.78831936
X-RAY DIFFRACTIONr_scangle_it2.8284.51752
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 160 -
Rwork0.196 2607 -
obs--93.35 %

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