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- PDB-2ev4: Structure of Rv1264N, the regulatory domain of the mycobacterial ... -

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Basic information

Entry
Database: PDB / ID: 2ev4
TitleStructure of Rv1264N, the regulatory domain of the mycobacterial adenylyl cylcase Rv1264, with a salt precipitant
ComponentsHypothetical protein Rv1264/MT1302
KeywordsLYASE / Alpha-helical / Regulatory Domain of Adenylyl cyclase / oleic acid
Function / homology
Function and homology information


adenylate cyclase inhibitor activity / adenylate cyclase / cAMP biosynthetic process / response to pH / adenylate cyclase activity / manganese ion binding / intracellular signal transduction / lipid binding / protein homodimerization activity / ATP binding
Similarity search - Function
Adenylate cyclase regulatory domain / Adenylate cyclase regulatory domain / : / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
OLEIC ACID / pH-sensitive adenylate cyclase Rv1264 / pH-sensitive adenylate cyclase Rv1264
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsFindeisen, F. / Tews, I. / Sinning, I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The structure of the regulatory domain of the adenylyl cyclase Rv1264 from Mycobacterium tuberculosis with bound oleic acid
Authors: Findeisen, F. / Linder, J.U. / Schultz, A. / Schultz, J.E. / Brugger, B. / Wieland, F. / Sinning, I. / Tews, I.
History
DepositionOct 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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 / _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 Rv1264/MT1302
B: Hypothetical protein Rv1264/MT1302
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9395
Polymers48,3392
Non-polymers6003
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-74 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.081, 53.916, 89.814
Angle α, β, γ (deg.)90.00, 132.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1004-

HOH

21A-1005-

HOH

31B-212-

HOH

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Components

#1: Protein Hypothetical protein Rv1264/MT1302 / ADENYLYL CYCLASE


Mass: 24169.354 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1264 / Plasmid: pQE 30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q11055, UniProt: P9WMU9*PLUS, adenylate cyclase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulphate, TRIS, lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 11, 2003
RadiationMonochromator: Khozu monochromator with a McLennon controller containing a LN2 cooled Si111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. all: 19629 / Num. obs: 18893 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.1
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1948 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.936 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26616 961 5.1 %RANDOM
Rwork0.21818 ---
all0.22069 19569 --
obs0.22069 17868 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.303 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å2-1.05 Å2
2--0.6 Å20 Å2
3----0.49 Å2
Refine analyzeLuzzati coordinate error obs: 0.437 Å
Refinement stepCycle: LAST / Resolution: 2.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 41 111 2969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222921
X-RAY DIFFRACTIONr_bond_other_d0.0020.022872
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9963948
X-RAY DIFFRACTIONr_angle_other_deg0.92636625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8155367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71423.684133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96115512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2531532
X-RAY DIFFRACTIONr_chiral_restr0.0730.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
X-RAY DIFFRACTIONr_nbd_refined0.2110.2699
X-RAY DIFFRACTIONr_nbd_other0.1980.23039
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21394
X-RAY DIFFRACTIONr_nbtor_other0.0830.21733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3570.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4050.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5740.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9721.52390
X-RAY DIFFRACTIONr_mcbond_other0.1581.5754
X-RAY DIFFRACTIONr_mcangle_it1.12422949
X-RAY DIFFRACTIONr_scbond_it2.03531169
X-RAY DIFFRACTIONr_scangle_it3.0284.5999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 77 -
Rwork0.289 1290 -
obs-1446 94.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
115.7694-4.69563.507615.0756-1.04312.66780.35080.0715-0.6309-0.2572-0.52060.26610.6463-1.44240.1698-0.24920.02450.03790.0451-0.0537-0.0351-26.6541-15.6695-14.0838
21.6449-0.49210.92194.8686-0.25744.61020.113-0.0455-0.3146-0.4445-0.23690.70420.7348-0.82430.1239-0.2082-0.16860.0243-0.0114-0.0521-0.0327-14.828-36.621.8379
37.4958-4.60847.86576.9846-6.773312.0181-0.2834-0.55280.2360.60650.51090.5785-0.7717-0.8437-0.2275-0.3007-0.00710.0928-0.2249-0.02-0.1703-9.4658-16.75384.2349
42.5502-0.46051.309410.73750.693221.3988-0.11280.42810.3454-0.785-0.2179-0.6157-1.60711.98130.3308-0.0099-0.09370.00190.18150.0871-0.107213.4449-38.407832.0635
52.9479-0.27321.26496.89780.90812.88720.0535-0.38670.18290.38430.0501-0.1802-0.1391-0.0099-0.1037-0.1934-0.01920.0228-0.1756-0.0833-0.285-1.4951-17.154517.4316
65.3839-5.46946.81677.5745-7.197711.33760.2175-0.3579-0.5877-0.01210.25120.57080.6309-0.147-0.4686-0.1954-0.07810.0513-0.2261-0.0063-0.2139-3.0245-37.726113.3022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 5623 - 68
2X-RAY DIFFRACTION2AA57 - 14969 - 161
3X-RAY DIFFRACTION3AA150 - 196162 - 208
4X-RAY DIFFRACTION4BB12 - 5624 - 68
5X-RAY DIFFRACTION5BB57 - 14969 - 161
6X-RAY DIFFRACTION6BB150 - 194162 - 206

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