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- PDB-2ev1: Structure of Rv1264N, the regulatory domain of the mycobacterial ... -

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Basic information

Entry
Database: PDB / ID: 2ev1
TitleStructure of Rv1264N, the regulatory domain of the mycobacterial adenylyl cylcase Rv1264, at pH 6.0
ComponentsHypothetical protein Rv1264/MT1302Hypothesis
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 / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / 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 / SAD / Resolution: 1.6 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 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)49,3806
Polymers48,3392
Non-polymers1,0414
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-73 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.600, 93.528, 54.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1105-

HOH

21B-1106-

HOH

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Components

#1: Protein Hypothetical protein Rv1264/MT1302 / Hypothesis / 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-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.3 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 200, MES, PEG 3000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Mar 14, 2003
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: 1.6→47 Å / Num. all: 58977 / Num. obs: 54058 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 5.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2 / Num. unique all: 7802 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.504 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21639 2706 5 %RANDOM
Rwork0.18759 ---
all0.18902 58799 --
obs0.18902 51196 91.67 %-
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: 29.326 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.83 Å20 Å2
3---0.47 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 1.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 63 353 3202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222932
X-RAY DIFFRACTIONr_bond_other_d0.0010.022906
X-RAY DIFFRACTIONr_angle_refined_deg1.4142.0023954
X-RAY DIFFRACTIONr_angle_other_deg1.3636710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8435364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81223.485132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47815514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8871533
X-RAY DIFFRACTIONr_chiral_restr0.0780.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined0.2260.2698
X-RAY DIFFRACTIONr_nbd_other0.1870.23005
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21438
X-RAY DIFFRACTIONr_nbtor_other0.0860.21741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.215
X-RAY DIFFRACTIONr_mcbond_it1.3111.52372
X-RAY DIFFRACTIONr_mcbond_other0.261.5748
X-RAY DIFFRACTIONr_mcangle_it1.48922934
X-RAY DIFFRACTIONr_scbond_it2.59931195
X-RAY DIFFRACTIONr_scangle_it3.944.51020
LS refinement shellResolution: 1.6→1.616 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.321 84 -
Rwork0.247 1499 -
obs-1701 93.06 %
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)
15.38514.99950.76389.13951.93065.2694-0.06080.0014-0.60730.06920.0658-0.2460.377-0.1008-0.005-0.1791-0.039-0.0242-0.155-0.0296-0.060632.1344-28.1213.2946
21.0679-0.8153-0.95631.42671.60664.5077-0.1594-0.2183-0.34610.43590.07570.34970.5381-0.19010.0837-0.0511-0.01670.0696-0.11650.075-0.092931.7055-12.887624.9588
31.0032-0.5077-0.52622.2775-0.13714.30920.0176-0.05660.0170.027-0.02680.2458-0.0644-0.31280.0092-0.1542-0.01980.0594-0.17630.0148-0.155928.0667-0.564619.8627
41.1272-0.9097-0.527711.3535.06994.12530.11620.1121-0.0325-0.4276-0.26580.45-0.1602-0.44510.1496-0.2526-0.0013-0.0192-0.15660.028-0.186333.5739-2.70923.6794
510.9825-8.217-1.007215.844-0.55457.74450.33350.47740.5279-0.852-0.2203-1.07160.12240.2857-0.1132-0.05130.0480.1491-0.105-0.03460.044433.490934.3725.3803
62.30270.18850.4662.7670.5843.3988-0.03740.11250.3945-0.02430.00230.2119-0.383-0.17190.0351-0.15910.02250.0008-0.14910.0685-0.093533.352918.66412.145
71.42490.2536-0.04052.23960.56745.28770.040.03980.10950.1148-0.00370.1692-0.0003-0.3078-0.0363-0.20270.0415-0.0182-0.19060.0419-0.152428.58276.59377.181
81.07910.79470.15512.54515.10923.06770.0496-0.20750.1650.7339-0.16960.44680.1396-0.2470.12-0.13660.03220.0469-0.14440.0098-0.156733.24369.541824.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 5523 - 67
2X-RAY DIFFRACTION2AA56 - 10768 - 119
3X-RAY DIFFRACTION3AA108 - 151120 - 163
4X-RAY DIFFRACTION4AA152 - 195164 - 207
5X-RAY DIFFRACTION5BB13 - 5525 - 67
6X-RAY DIFFRACTION6BB56 - 10768 - 119
7X-RAY DIFFRACTION7BB108 - 151120 - 163
8X-RAY DIFFRACTION8BB152 - 193164 - 205

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