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- PDB-2ev3: Structure of Rv1264N, the regulatory domain of the mycobacterial ... -

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Basic information

Entry
Database: PDB / ID: 2ev3
TitleStructure of Rv1264N, the regulatory domain of the mycobacterial adenylyl cylcase Rv1264, at pH 5.3
ComponentsHypothetical protein Rv1264/MT1302Hypothesis
KeywordsLYASE / Alpha-helical / Regulatory Domain of Adenylyl cyclase
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 / MOLECULAR REPLACEMENT / Resolution: 2.68 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 / 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)48,9044
Polymers48,3392
Non-polymers5652
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-77 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.403, 52.976, 89.399
Angle α, β, γ (deg.)90.00, 133.73, 90.00
Int Tables number5
Space group name H-MC121

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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: pQE30 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.1 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG 400, sodium acetate, calcium acetate, pH 5.3, 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: 2.68→45 Å / Num. all: 11634 / Num. obs: 11593 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 90.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.4
Reflection shellResolution: 2.68→2.82 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1665 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 36.521 / SU ML: 0.337 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26517 551 4.8 %RANDOM
Rwork0.22927 ---
all0.23084 11634 --
obs0.23084 11038 99.66 %-
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: 79.249 Å2
Baniso -1Baniso -2Baniso -3
1-3.77 Å20 Å25.3 Å2
2---3.59 Å20 Å2
3---7.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.517 Å
Refinement stepCycle: LAST / Resolution: 2.68→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2819 0 40 22 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222893
X-RAY DIFFRACTIONr_bond_other_d00.022825
X-RAY DIFFRACTIONr_angle_refined_deg0.9571.9973911
X-RAY DIFFRACTIONr_angle_other_deg3.26936515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4225367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89623.939132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83215496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0421530
X-RAY DIFFRACTIONr_chiral_restr0.0580.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02541
X-RAY DIFFRACTIONr_nbd_refined0.1860.2628
X-RAY DIFFRACTIONr_nbd_other0.2410.22571
X-RAY DIFFRACTIONr_nbtor_refined0.1540.21381
X-RAY DIFFRACTIONr_nbtor_other0.0980.21559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0460.21
X-RAY DIFFRACTIONr_mcbond_it2.4741.52386
X-RAY DIFFRACTIONr_mcbond_other0.5031.5754
X-RAY DIFFRACTIONr_mcangle_it2.88322927
X-RAY DIFFRACTIONr_scbond_it5.531140
X-RAY DIFFRACTIONr_scangle_it8.2874.5984
LS refinement shellResolution: 2.68→2.824 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.382 88 -
Rwork0.359 1569 -
obs-1569 99.7 %
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)
117.3-4.0678-1.88239.86255.97436.9983-0.21720.96130.937-0.1318-0.3091-0.0639-0.06390.56610.5263-0.11340.075-0.08850.1450.1287-0.189227.2959-10.7189-14.3568
22.6323-0.3925-2.11677.35211.27514.82810.10790.0540.2097-0.45650.0877-0.5745-0.47510.7087-0.1955-0.257-0.1486-0.0831-0.0733-0.0313-0.132215.30117.5282.1166
37.3297-4.5213-7.67356.74765.31299.2303-0.4826-0.2738-0.60940.07410.10350.24830.40210.57630.3791-0.3223-0.0303-0.0609-0.18530.1083-0.03497.9572-8.09044.2336
41.47972.8906-1.05466.29731.079115.90230.03670.03720.1133-0.1765-0.16350.59410.428-0.9570.1268-0.12040.0557-0.00870.0909-0.0167-0.0354-14.909111.412830.8169
53.2063-0.7458-1.08774.7174-0.38761.9028-0.0041-0.4309-0.20910.3041-0.0393-0.05830.17960.14240.0434-0.1969-0.0027-0.059-0.13620.1068-0.21631.0264-7.425317.3661
67.6371-5.8077-8.40538.0856.801110.99650.0499-0.28860.32570.01090.2275-0.305-0.24190.315-0.2775-0.2457-0.0758-0.1224-0.19880.0698-0.27923.14068.464410.4993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 5624 - 68
2X-RAY DIFFRACTION2AA57 - 15669 - 168
3X-RAY DIFFRACTION3AA157 - 195169 - 207
4X-RAY DIFFRACTION4BB12 - 5624 - 68
5X-RAY DIFFRACTION5BB57 - 15669 - 168
6X-RAY DIFFRACTION6BB157 - 195169 - 207

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