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- PDB-3ib8: Crystal structure of full length Rv0805 in complex with 5'-AMP -

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Basic information

Entry
Database: PDB / ID: 3ib8
TitleCrystal structure of full length Rv0805 in complex with 5'-AMP
ComponentsIcc protein
KeywordsHYDROLASE / metallophosphoesterase / alpha-beta fold / swapped-dimer
Function / homology
Function and homology information


: / 2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / cell wall modification / cell envelope / 3',5'-cyclic-nucleotide phosphodiesterase / phosphate ion binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / ferric iron binding ...: / 2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / cell wall modification / cell envelope / 3',5'-cyclic-nucleotide phosphodiesterase / phosphate ion binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / ferric iron binding / peptidoglycan-based cell wall / manganese ion binding / iron ion binding / nucleotide binding / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Cyclic nucleotide phosphodiesterase GpdQ/CpdA-like / : / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / : / : / cAMP/cGMP dual specificity phosphodiesterase MT0825 / cAMP/cGMP dual specificity phosphodiesterase Rv0805
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPodobnik, M. / Dermol, U.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability
Authors: Podobnik, M. / Tyagi, R. / Matange, N. / Dermol, U. / Gupta, A.K. / Mattoo, R. / Seshadri, K. / Visweswariah, S.S.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis
Authors: Shenoy, A.R. / Capuder, M. / Draskovic, P. / Lamba, D. / Visweswariah, S.S. / Podobnik, M.
#2: Journal: Biochemistry / Year: 2005
Title: The Rv0805 gene from Mycobacterium tuberculosis encodes a 3',5'-cyclic nucleotide phosphodiesterase: biochemical and mutational analysis
Authors: Shenoy, A.R. / Sreenath, N. / Podobnik, M. / Kovacevic, M. / Visweswariah, S.S.
History
DepositionJul 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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.value / _struct_conn.pdbx_dist_value / _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_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: Icc protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6079
Polymers35,5261
Non-polymers1,0818
Water4,450247
1
A: Icc protein
hetero molecules

A: Icc protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,21418
Polymers71,0532
Non-polymers2,16216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10950 Å2
ΔGint-152 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.400, 100.400, 80.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Icc protein / Rv0805 phosphodiesterase protein


Mass: 35526.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0805 / Plasmid: pProExHTc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O06629, UniProt: P9WP65*PLUS, 3',5'-cyclic-nucleotide phosphodiesterase

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Non-polymers , 7 types, 255 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.87 Å3/Da / Density % sol: 57.08 % / Mosaicity: 0.303 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Bis-Tris, amm. acetate, MPD, AMP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9864 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 28, 2006 / Details: mirrors
RadiationMonochromator: Fixed exit double crystal (Si), horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9864 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 38865 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.001 / Net I/σ(I): 9.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2546 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IB7

3ib7


Resolution: 1.8→31.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.066 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.168 3868 10 %RANDOM
Rwork0.15 ---
all0.217 45158 --
obs0.152 38804 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.68 Å2 / Biso mean: 27.65 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 67 247 2543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212337
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9993186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4915294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90822.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8021523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021766
X-RAY DIFFRACTIONr_nbd_refined0.1880.21064
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.234
X-RAY DIFFRACTIONr_mcbond_it0.4011.51506
X-RAY DIFFRACTIONr_mcangle_it0.6422352
X-RAY DIFFRACTIONr_scbond_it1.2793918
X-RAY DIFFRACTIONr_scangle_it2.0784.5834
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 277 -
Rwork0.204 2537 -
all-2814 -
obs--99.96 %
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)
117.39573.98664.152514.8299-3.03134.735-0.02041.13511.1209-1.1974-0.16370.5885-0.7779-1.38440.18410.03160.0689-0.02380.03520.09990.004914.112134.9658-18.1885
26.6661-4.35-0.036310.2771-2.81023.37070.24830.22850.0448-0.33080.02760.4183-0.343-0.2185-0.2758-0.0938-0.0006-0.002-0.0770.0305-0.141823.620523.2453-17.9726
31.0511-0.63480.13974.6106-3.28063.24340.01130.0493-0.2176-0.21690.0930.22310.2358-0.109-0.1043-0.137-0.004-0.0381-0.13850.0086-0.09722.2676-1.6452-2.7418
41.3201-1.0731.23987.0642-10.887316.92760.03240.0708-0.3408-0.20990.18620.51780.2384-0.5276-0.2186-0.0729-0.036-0.0495-0.12920.0018-0.032415.4925-2.6114-4.8256
515.7538-0.79885.310715.6823-16.749119.1530.50910.8644-0.4104-1.2223-0.11830.46450.79390.1939-0.3908-0.0190.0173-0.0757-0.0532-0.0657-0.051814.10715.355-15.9412
60.89550.1007-0.17033.0523-1.39011.06240.03910.2229-0.1504-0.4341-0.0472-0.02390.27250.00360.0081-0.08490.0142-0.0072-0.1065-0.0043-0.102327.37940.6403-9.0352
72.5581.12641.798924.9828-8.107911.3820.26950.4696-0.0945-1.2406-0.01070.57280.3886-0.0488-0.25880.0420.0413-0.0342-0.0196-0.0161-0.105224.52973.2498-18.5195
82.6945-0.7838-0.80581.42610.30733.0421-0.0250.0977-0.337-0.17940.0117-0.10490.25070.2390.0133-0.12580.02260.0052-0.12130.009-0.061334.87590.3515-4.455
921.17910.2666-12.833418.679212.026415.7302-0.30870.9739-1.2225-1.0703-0.7430.5292-0.1141-0.40091.0517-0.01480.04760.01960.0221-0.09930.085437.4504-4.6049-11.8028
100.73270.7411-0.60162.5165-1.76031.7349-0.01540.0716-0.1591-0.2054-0.0503-0.17250.31180.20810.0657-0.12410.0146-0.0092-0.09950.033-0.044838.93997.6964-4.8478
116.6063.1426-5.95082.4925-2.57565.426-0.0113-0.3658-0.480.0002-0.2283-0.27720.23330.39910.2395-0.1332-0.0155-0.0453-0.05760.0492-0.030444.905112.10541.1525
120.75940.6784-0.83210.9748-1.03082.7920.0640.03110.01190.06220.0128-0.0799-0.0431-0.0155-0.0768-0.16240.0023-0.016-0.12640.0317-0.103234.980217.4136-2.2934
137.85452.4899-3.24945.3027-3.64125.692-0.1278-0.5321-0.21790.1667-0.0419-0.26220.1410.16860.1697-0.0750.0003-0.0455-0.09730.0358-0.116532.437910.480712.7858
141.70030.8585-1.06112.053-1.41131.54250.07270.00640.11930.2196-0.022-0.1424-0.19440.1278-0.0507-0.12480.0072-0.0242-0.11880.0232-0.12934.85918.78350.6637
151.84050.62130.51751.7160.10560.5550.0417-0.1559-0.04760.1449-0.02860.06380.0287-0.0259-0.0131-0.139-0.0026-0.0145-0.14860.0245-0.132920.148511.41713.9978
1613.0691-0.66322.11289.33781.21811.70740.16810.35250.3437-0.0602-0.15380.1196-0.3989-0.0816-0.0143-0.12230.00990.0043-0.12460.0485-0.14324.640325.8535-13.2879
175.66492.3808-0.96663.0592-0.6931.0724-0.04560.0948-0.1495-0.20710.04890.04910.1299-0.0221-0.0033-0.13790.0018-0.0228-0.14160.0146-0.150316.567315.865-6.8536
185.26934.3686-9.68744.5452-11.424130.275-0.27330.7677-0.2314-0.74080.3840.24160.2927-0.9877-0.11070.0942-0.0374-0.12140.010.0180.00050.493116.5583-15.74
1928.209516.5953-6.863686.5551-4.10712.0184-0.84142.20071.4961-2.84510.87691.70860.4488-0.9157-0.03550.1339-0.0265-0.18820.1010.0897-0.04194.2425.3557-23.1397
2045.4259-20.90014.224112.9546-0.91950.70690.79591.61290.1206-1.1791-0.6510.2202-0.18670.4039-0.14490.18840.0295-0.05710.27390.151-0.014616.412129.0604-22.9251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 9
2X-RAY DIFFRACTION2A10 - 15
3X-RAY DIFFRACTION3A16 - 32
4X-RAY DIFFRACTION4A33 - 44
5X-RAY DIFFRACTION5A45 - 51
6X-RAY DIFFRACTION6A52 - 77
7X-RAY DIFFRACTION7A78 - 90
8X-RAY DIFFRACTION8A91 - 105
9X-RAY DIFFRACTION9A106 - 111
10X-RAY DIFFRACTION10A112 - 141
11X-RAY DIFFRACTION11A142 - 153
12X-RAY DIFFRACTION12A154 - 177
13X-RAY DIFFRACTION13A178 - 188
14X-RAY DIFFRACTION14A189 - 209
15X-RAY DIFFRACTION15A210 - 252
16X-RAY DIFFRACTION16A253 - 257
17X-RAY DIFFRACTION17A258 - 269
18X-RAY DIFFRACTION18A270 - 280
19X-RAY DIFFRACTION19A281 - 285
20X-RAY DIFFRACTION20A286 - 298

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