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- PDB-3ib7: Crystal structure of full length Rv0805 -

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Basic information

Entry
Database: PDB / ID: 3ib7
TitleCrystal structure of full length Rv0805
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 / : / : / 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 / molecular replacement / Resolution: 1.6 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
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.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.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)36,2018
Polymers35,5261
Non-polymers6747
Water5,260292
1
A: Icc protein
hetero molecules

A: Icc protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,40216
Polymers71,0532
Non-polymers1,34914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9410 Å2
ΔGint-114 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.178, 100.178, 80.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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 , 6 types, 299 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.83 Å3/Da / Density % sol: 56.59 % / Mosaicity: 0.217 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Bis-Tris, amm. acetate, MPD, pH 6.5, 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: 1.008 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: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 54354 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.4 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.057 / Χ2: 1.001 / Net I/σ(I): 11.6
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3547 / Χ2: 1.003 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å32.4 Å
Translation1.6 Å32.4 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3phasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HY1

2hy1


Resolution: 1.6→32.4 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.262 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 5463 10.1 %RANDOM
Rwork0.159 ---
all0.218 64774 --
obs0.161 54293 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.04 Å2 / Biso mean: 25.518 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.76 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 40 292 2561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212308
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9843141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4135294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92622.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94215354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8231523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021759
X-RAY DIFFRACTIONr_nbd_refined0.1930.21041
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.236
X-RAY DIFFRACTIONr_mcbond_it0.3821.51508
X-RAY DIFFRACTIONr_mcangle_it0.62922354
X-RAY DIFFRACTIONr_scbond_it1.2263875
X-RAY DIFFRACTIONr_scangle_it2.0124.5787
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 412 -
Rwork0.311 3505 -
all-3917 -
obs--99.11 %
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)
13.91950.2358-1.66480.4232-0.18831.48110.0901-0.1060.26380.11880.04360.0467-0.097-0.065-0.1337-0.0989-0.00030.0207-0.1405-0.0126-0.120133.604128.938412.0431
217.9001-0.00756.15663.3938-0.37437.9814-0.112-0.64680.74250.11710.0441-0.3458-0.45480.04190.0679-0.1143-0.00490.0201-0.1128-0.0478-0.025959.877631.3109-1.1155
310.9667-1.9068-12.07971.72091.833713.49780.129-0.55740.47190.13490.1966-0.2347-0.25930.5795-0.3256-0.1133-0.0133-0.0182-0.0723-0.0438-0.058850.065135.26149.0086
42.44525.0562-0.511911.4587-1.38160.21120.1292-0.37110.46090.7371-0.08820.2911-0.13880.0874-0.041-0.0136-0.00660.0139-0.0323-0.0276-0.073338.306928.668918.3917
52.7066-0.6382-0.97991.2770.68131.4506-0.0627-0.4728-0.00240.18470.0904-0.12250.03990.2611-0.0277-0.10650.007-0.002-0.0719-0.0102-0.098752.430222.62749.129
63.0781-0.914-2.55232.46881.42956.1383-0.0938-0.4150.10610.2920.1101-0.150.08920.1974-0.0164-0.12570.0217-0.0191-0.0877-0.0113-0.100646.423919.97969.3215
77.7161.3763.63975.2440.42453.3781-0.113-0.3297-0.15460.3771-0.0732-0.54660.13040.21510.1861-0.06160.0439-0.0011-0.0630.0434-0.003152.491110.19967.6499
811.1324-6.3893-15.70563.6679.01422.15740.264-0.52730.57210.00610.2457-0.3505-0.17320.9403-0.5096-0.0824-0.01110.0298-0.03460.0008-0.03337.486911.816314.2615
93.53790.8219-3.32630.7329-0.80143.7606-0.02530.0358-0.06740.01720.0405-0.09510.08590.0767-0.0152-0.1420.00520.0198-0.1427-0.019-0.086841.109813.07042.2173
103.36338.3559-5.911630.9573-16.349510.6616-0.41490.106-0.5809-0.611-0.2816-1.32850.55090.4190.6965-0.0425-0.03430.0383-0.102-0.01130.01940.91036.1215-4.5517
116.1541-0.435-6.24160.52940.6326.4034-0.08920.0719-0.1280.01830.0575-0.11810.1592-0.00490.0316-0.0903-0.00590.0232-0.1338-0.0031-0.075632.91884.46634.72
120.82650.4471-0.67020.7152-0.2780.7240.05680.0560.00250.06110.02640.0599-0.1149-0.0608-0.0832-0.1329-0.00040.0242-0.1396-0.0041-0.114933.731218.38670.8871
134.89584.506-3.91067.5605-3.99284.3956-0.02930.2071-0.2338-0.3377-0.1186-0.16920.20.0470.148-0.11440.00570.0103-0.0809-0.0246-0.11338.411516.3084-11.5535
1415.79862.6764-10.10016.8088-1.680921.754-0.23650.9789-0.3864-0.363-0.00160.05530.5212-1.06360.2382-0.1007-0.03210.0273-0.0846-0.0496-0.074126.46918.833-2.8664
151.63620.3335-0.26771.18290.11090.409-0.03140.1330.0746-0.07830.02650.07380.015-0.01230.005-0.137-0.00010.0055-0.1344-0.0081-0.137936.106325.7129-3.0993
163.52861.3534-2.12361.8761-1.06112.17770.0277-0.04780.1010.07240.01570.0395-0.0246-0.0037-0.0435-0.14730.00590.0046-0.154-0.0077-0.136735.629831.50344.6151
175.8225-3.6985-1.86369.7712-5.28219.77250.0881-0.69480.42960.46350.3308-0.3826-0.43830.1506-0.4189-0.0721-0.0325-0.0115-0.0447-0.0859-0.050336.951250.549910.5767
1827.82976.1943-10.56133.2496-2.338217.75550.3265-1.34940.81110.4264-0.17180.0656-0.33280.5896-0.15470.03360.0097-0.02760.0232-0.0764-0.059828.729946.792222.7916
1958.80573.9911-9.50797.373-1.14463.55260.0285-1.04481.73580.5524-0.01280.679-0.2536-0.0209-0.01570.00810.02720.0396-0.0215-0.07230.006419.882646.666121.9302
2016.5999-28.2342-0.96554.833.04490.3455-0.8067-0.8089-0.30972.02390.89860.44520.4044-0.2218-0.09190.26940.09760.10280.04070.0266-0.058822.020730.136822.9115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 27
2X-RAY DIFFRACTION2A28 - 32
3X-RAY DIFFRACTION3A33 - 50
4X-RAY DIFFRACTION4A51 - 58
5X-RAY DIFFRACTION5A59 - 85
6X-RAY DIFFRACTION6A86 - 100
7X-RAY DIFFRACTION7A101 - 119
8X-RAY DIFFRACTION8A120 - 124
9X-RAY DIFFRACTION9A125 - 141
10X-RAY DIFFRACTION10A142 - 147
11X-RAY DIFFRACTION11A148 - 158
12X-RAY DIFFRACTION12A159 - 177
13X-RAY DIFFRACTION13A178 - 191
14X-RAY DIFFRACTION14A192 - 197
15X-RAY DIFFRACTION15A198 - 239
16X-RAY DIFFRACTION16A240 - 266
17X-RAY DIFFRACTION17A267 - 275
18X-RAY DIFFRACTION18A276 - 283
19X-RAY DIFFRACTION19A284 - 289
20X-RAY DIFFRACTION20A290 - 298

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