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- PDB-1y10: Mycobacterial adenylyl cyclase Rv1264, holoenzyme, inhibited state -

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Basic information

Entry
Database: PDB / ID: 1y10
TitleMycobacterial adenylyl cyclase Rv1264, holoenzyme, inhibited state
ComponentsHypothetical protein Rv1264/MT1302Hypothesis
KeywordsLYASE / adenylyl cyclase fold
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 / Nucleotide cyclase, GGDEF 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
pH-sensitive adenylate cyclase Rv1264 / pH-sensitive adenylate cyclase Rv1264
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTews, I. / Findeisen, F. / Sinning, I. / Schultz, A. / Schultz, J.E. / Linder, J.U.
CitationJournal: Science / Year: 2005
Title: The structure of a pH-sensing mycobacterial adenylyl cyclase holoenzyme
Authors: Tews, I. / Findeisen, F. / Sinning, I. / Schultz, A. / Schultz, J.E. / Linder, J.U.
History
DepositionNov 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 23, 2014Group: Other
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 / 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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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
C: Hypothetical protein Rv1264/MT1302
D: Hypothetical protein Rv1264/MT1302
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,01615
Polymers173,9814
Non-polymers1,03511
Water9,404522
1
A: Hypothetical protein Rv1264/MT1302
B: Hypothetical protein Rv1264/MT1302
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6278
Polymers86,9902
Non-polymers6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13100 Å2
ΔGint-135 kcal/mol
Surface area29850 Å2
MethodPISA
2
C: Hypothetical protein Rv1264/MT1302
D: Hypothetical protein Rv1264/MT1302
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3897
Polymers86,9902
Non-polymers3995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-133 kcal/mol
Surface area29730 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30370 Å2
ΔGint-279 kcal/mol
Surface area54760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.936, 146.830, 84.849
Angle α, β, γ (deg.)90.00, 105.26, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit is composed of two biological dimers. A and B form one dimer, C and D the other one.

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Components

#1: Protein
Hypothetical protein Rv1264/MT1302 / Hypothesis / adenylyl cyclase


Mass: 43495.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1264 / Plasmid: pQE60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: Q11055, UniProt: P9WMU9*PLUS, adenylate cyclase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 40.7 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: PEG400, calcium acetate, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 64787 / Num. obs: 63500 / % possible obs: 98 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -4 / Redundancy: 6.1 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.9
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 2 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1802 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rv1264 RESIDUES 1-207 (to be deposited)

Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 15.893 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.396 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 3191 5 %RANDOM
Rwork0.19023 ---
all0.19287 61314 --
obs0.19287 60069 97.97 %-
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: 46.756 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-1.44 Å2
2--0.15 Å20 Å2
3----0.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.359 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10803 0 56 522 11381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211012
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210692
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.98114944
X-RAY DIFFRACTIONr_angle_other_deg1.469324547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01851428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45122.668476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.665151775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.54915131
X-RAY DIFFRACTIONr_chiral_restr0.0760.21738
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212409
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022238
X-RAY DIFFRACTIONr_nbd_refined0.190.22333
X-RAY DIFFRACTIONr_nbd_other0.2040.29970
X-RAY DIFFRACTIONr_nbtor_refined0.1630.25214
X-RAY DIFFRACTIONr_nbtor_other0.080.26577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2386
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0460.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1151.57354
X-RAY DIFFRACTIONr_mcbond_other0.2381.52939
X-RAY DIFFRACTIONr_mcangle_it1.641211354
X-RAY DIFFRACTIONr_scbond_it2.74634113
X-RAY DIFFRACTIONr_scangle_it4.3314.53590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.323 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.374 88 -
Rwork0.273 1493 -
obs--84.19 %
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)
13.7572-1.0568-1.3613.5624-0.83183.3230.05320.77320.2165-0.67890.0149-0.08140.1657-0.0477-0.0682-0.1517-0.05130.01650.0008-0.0086-0.166323.229653.43931.501
22.18930.82620.05012.87120.54931.0134-0.0371-0.2246-0.00010.15-0.04940.12140.0167-0.08320.0865-0.23020.0249-0.0223-0.0940.0071-0.25072.935455.926553.0251
33.6827-2.1836-6.56692.16213.795111.72110.33690.04450.18540.0205-0.1282-0.2463-0.409-0.1758-0.2087-0.1771-0.0449-0.0872-0.08510.0254-0.028521.570165.585451.1588
44.5426-0.77110.90664.5935-0.35264.0086-0.1641-0.03150.24120.17360.07730.1134-0.2627-0.12880.0868-0.00080.0299-0.0077-0.1988-0.0067-0.11044.449591.91263.3396
514.9011.7788-1.810517.2139-3.08077.5924-0.1914-0.3031-0.4775-0.1778-0.2827-0.08590.3887-0.14340.47420.13950.13750.00480.0481-0.0808-0.0292-8.669196.877265.3836
66.90.2102-5.96843.86110.288118.04250.2914-1.04471.32120.1961-0.08750.8606-1.9693-1.8616-0.2040.21430.213-0.02780.439-0.21430.19816.315171.515288.4206
71.61240.5116-0.2321.8513-0.07842.9723-0.0195-0.07240.03310.117-0.0892-0.3227-0.30930.23550.1087-0.0466-0.0222-0.0618-0.1641-0.0231-0.035420.569378.296662.0806
81.1346-0.0489-2.40411.19270.127217.67730.10810.06080.12280.30220.01690.1576-0.4097-1.705-0.125-0.07990.0312-0.0079-0.0195-0.0105-0.12043.898863.408769.9311
94.3013-0.59510.07173.0862-0.59312.8161-0.0056-0.13110.2723-0.01490.02470.2284-0.2597-0.0193-0.0192-0.2651-0.0168-0.0076-0.25520.024-0.2066-3.782568.039337.6089
1028.2593-2.36261.59665.6494-3.14429.0881-0.21660.60250.8667-0.53410.25390.0321-0.45370.456-0.03730.12720.0088-0.0649-0.1636-0.0611-0.1096-4.34978.132627.7193
117.35311.2588-0.56956.38410.46553.9811-0.0179-1.050.60930.6508-0.11160.0666-0.86070.33210.12950.1504-0.0735-0.00750.0027-0.096-0.102533.01577.04786.7865
123.6749-0.1030.223.79551.8424.1778-0.11060.1671-0.1228-0.00570.12710.08470.12930.0326-0.0165-0.1298-0.0556-0.0066-0.14210.0423-0.271320.305751.135379.8475
132.60617.9324.731824.851215.790211.31010.42380.0602-0.53330.21570.3773-1.4868-0.29950.4449-0.8011-0.0835-0.03260.015-0.0458-0.0108-0.084736.002564.202969.9923
146.10080.50060.01164.4772-0.90571.95810.0852-0.6452-0.09040.4095-0.2665-0.24450.02240.15650.1813-0.18950.00270.0479-0.17220.0488-0.223243.972432.983258.5585
1533.7904-2.8514-6.51486.786-0.78327.54980.0408-0.3857-0.35910.0877-0.1022-0.0660.39950.08780.06150.0203-0.0356-0.0289-0.15760.1461-0.055843.785819.055561.8128
163.709-0.05691.2693.6429-0.6784.21650.11070.2762-0.6547-0.20530.1166-0.06780.4801-0.0399-0.2273-0.1638-0.02220.0101-0.1145-0.0811-0.12516.850434.168543.6151
172.95310.7523-0.46112.3856-0.55683.75720.0392-0.20510.39580.31720.0318-0.07-0.15890.1994-0.071-0.21220.03630.0225-0.1789-0.0548-0.130837.362252.38955.3102
184.76657.07216.812810.600610.386710.45740.6757-0.4107-0.50511.0085-0.3721-0.50840.8352-0.6242-0.3036-0.0911-0.0018-0.0212-0.04550.0189-0.128817.687243.407662.8607
193.8986-1.5730.03775.8015-1.6792.9919-0.13310.1462-0.3095-0.2923-0.0149-0.3090.34440.240.148-0.11960.00020.0408-0.11370.0256-0.19937.000545.692190.9469
2012.2405-0.2860.071421.3866-11.443616.6154-0.16530.40090.14430.06380.0493-1.4056-0.2961.09950.116-0.00650.04980.0350.1624-0.12430.263951.171644.296893.7614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 6014 - 60
2X-RAY DIFFRACTION2AA61 - 14961 - 149
3X-RAY DIFFRACTION3AA159 - 190159 - 190
4X-RAY DIFFRACTION4AA191 - 345191 - 345
5X-RAY DIFFRACTION5AA349 - 376349 - 376
6X-RAY DIFFRACTION6BB20 - 6020 - 60
7X-RAY DIFFRACTION7BB61 - 14961 - 149
8X-RAY DIFFRACTION8BB150 - 190150 - 190
9X-RAY DIFFRACTION9BB191 - 348191 - 348
10X-RAY DIFFRACTION10BB349 - 376349 - 376
11X-RAY DIFFRACTION11CC12 - 6012 - 60
12X-RAY DIFFRACTION12CC61 - 14961 - 149
13X-RAY DIFFRACTION13CC150 - 190150 - 190
14X-RAY DIFFRACTION14CC191 - 345191 - 345
15X-RAY DIFFRACTION15CC349 - 377349 - 377
16X-RAY DIFFRACTION16DD14 - 6014 - 60
17X-RAY DIFFRACTION17DD61 - 14961 - 149
18X-RAY DIFFRACTION18DD150 - 190150 - 190
19X-RAY DIFFRACTION19DD191 - 346191 - 346
20X-RAY DIFFRACTION20DD350 - 376350 - 376

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