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- PDB-4yf6: Crystal structure of oxidised Rv1284 -

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Basic information

Entry
Database: PDB / ID: 4yf6
TitleCrystal structure of oxidised Rv1284
ComponentsBeta-carbonic anhydrase 1
KeywordsLYASE / beta-carbonic anhydrase
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
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
Beta-carbonic anhydrase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsHofmann, A.
CitationJournal: Febs J. / Year: 2015
Title: Chemical probing suggests redox-regulation of the carbonic anhydrase activity of mycobacterial Rv1284.
Authors: Nienaber, L. / Cave-Freeman, E. / Cross, M. / Mason, L. / Bailey, U.M. / Amani, P. / A Davis, R. / Taylor, P. / Hofmann, A.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-carbonic anhydrase 1
B: Beta-carbonic anhydrase 1
C: Beta-carbonic anhydrase 1
D: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,40512
Polymers77,0234
Non-polymers3818
Water181
1
A: Beta-carbonic anhydrase 1
B: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7026
Polymers38,5122
Non-polymers1914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-138 kcal/mol
Surface area12930 Å2
MethodPISA
2
C: Beta-carbonic anhydrase 1
D: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7026
Polymers38,5122
Non-polymers1914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-134 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.068, 153.947, 157.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein
Beta-carbonic anhydrase 1 / Beta-CA 1 / Carbonate dehydratase 1 / mtCA 1


Mass: 19255.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: mtcA1, canA, MT1322 / Plasmid: pCR T7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21AI / References: UniProt: P9WPJ6, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M NaF, 20% PEG 3500, 0.1 M Bis-TRIS propane, soaked with 10 mM H2O2 for 10 min

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95375 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 3→24.4 Å / Num. obs: 23594 / % possible obs: 99.7 % / Redundancy: 14.9 % / Rsym value: 0.207 / Net I/σ(I): 3.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLK

1ylk


Resolution: 3.002→24.391 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 28.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1153 4.89 %
Rwork0.1667 --
obs0.1714 23594 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.002→24.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 8 1 5093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095220
X-RAY DIFFRACTIONf_angle_d1.1727100
X-RAY DIFFRACTIONf_dihedral_angle_d14.7761948
X-RAY DIFFRACTIONf_chiral_restr0.042824
X-RAY DIFFRACTIONf_plane_restr0.006928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0021-3.13840.35671660.26842759X-RAY DIFFRACTION99
3.1384-3.30350.32481500.24412805X-RAY DIFFRACTION100
3.3035-3.50990.33191600.20642781X-RAY DIFFRACTION100
3.5099-3.780.3281170.17232827X-RAY DIFFRACTION100
3.78-4.15870.26791650.15332799X-RAY DIFFRACTION100
4.1587-4.75670.20081200.1232817X-RAY DIFFRACTION100
4.7567-5.97830.18421460.13092817X-RAY DIFFRACTION100
5.9783-24.39160.17591290.12492836X-RAY DIFFRACTION100

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