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- PDB-4j6o: Crystal Structure of the Phosphatase Domain of C. thermocellum (B... -

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Basic information

Entry
Database: PDB / ID: 4j6o
TitleCrystal Structure of the Phosphatase Domain of C. thermocellum (Bacterial) PnkP
ComponentsMetallophosphoesterase
KeywordsHYDROLASE / Alpha/Beta fold / calcineurin-like / Phosphatase / metalloenzyme
Function / homology
Function and homology information


phosphatase activity / GTP binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / : / AAA domain / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type ...Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / : / AAA domain / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / 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 / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / : / TRIETHYLENE GLYCOL / Metallophosphoesterase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsWang, L. / Smith, P. / Shuman, S.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system.
Authors: Wang, L.K. / Smith, P. / Shuman, S.
History
DepositionFeb 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Feb 28, 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_asym_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_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: Metallophosphoesterase
B: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,58419
Polymers59,4282
Non-polymers2,15617
Water6,359353
1
A: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,96810
Polymers29,7141
Non-polymers1,2549
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6169
Polymers29,7141
Non-polymers9028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.700, 38.660, 92.950
Angle α, β, γ (deg.)90.00, 91.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallophosphoesterase


Mass: 29713.896 Da / Num. of mol.: 2 / Fragment: phosphatase domain (residues 171-424)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2768 / Plasmid: pET28-smt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A3DJ38, protein-serine/threonine phosphatase

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Non-polymers , 6 types, 370 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Polyethylene Glycol, Citrate Buffer, DMSO, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2013
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 63751 / Num. obs: 62980 / % possible obs: 98.8 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.039 / Net I/σ(I): 19.4
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.75 % / Mean I/σ(I) obs: 2.04 / Rsym value: 0.506 / % possible all: 89.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX1.8.1_1168refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→38.687 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 3099 5.06 %
Rwork0.1637 --
obs0.1658 61227 96.09 %
all-63133 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→38.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 138 353 4575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134417
X-RAY DIFFRACTIONf_angle_d1.5075924
X-RAY DIFFRACTIONf_dihedral_angle_d15.021691
X-RAY DIFFRACTIONf_chiral_restr0.1637
X-RAY DIFFRACTIONf_plane_restr0.007766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62010.23961040.24781844X-RAY DIFFRACTION68
1.6201-1.64660.31051110.23712155X-RAY DIFFRACTION79
1.6466-1.6750.24471110.23092410X-RAY DIFFRACTION86
1.675-1.70550.27881430.21932459X-RAY DIFFRACTION92
1.7055-1.73830.27061340.20522641X-RAY DIFFRACTION97
1.7383-1.77380.23311460.18692707X-RAY DIFFRACTION99
1.7738-1.81230.23341480.18542699X-RAY DIFFRACTION100
1.8123-1.85450.21051580.18992753X-RAY DIFFRACTION100
1.8545-1.90090.27311590.19332698X-RAY DIFFRACTION100
1.9009-1.95230.20131450.17892723X-RAY DIFFRACTION100
1.9523-2.00970.24961560.17872738X-RAY DIFFRACTION100
2.0097-2.07460.23811350.18212719X-RAY DIFFRACTION100
2.0746-2.14870.23281320.17862785X-RAY DIFFRACTION100
2.1487-2.23470.22561540.18182681X-RAY DIFFRACTION100
2.2347-2.33640.25361330.18032753X-RAY DIFFRACTION100
2.3364-2.45960.20771380.17552758X-RAY DIFFRACTION100
2.4596-2.61370.23271670.18372719X-RAY DIFFRACTION99
2.6137-2.81540.24021460.1722735X-RAY DIFFRACTION99
2.8154-3.09860.18941450.16882758X-RAY DIFFRACTION99
3.0986-3.54680.17961550.1512746X-RAY DIFFRACTION99
3.5468-4.46750.16411520.12672784X-RAY DIFFRACTION99
4.4675-38.69860.1911270.15232863X-RAY DIFFRACTION98
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)
10.126-0.01060.11850.38371.31854.88650.1985-0.154-0.00070.4357-0.54150.1659-1.3721-0.2625-0.12820.5711-0.0603-0.03160.28140.09760.721253.998140.391231.1253
21.8742-0.3352-0.36641.332-1.36921.71060.1624-0.41440.05940.3933-0.1422-0.3759-0.21090.1395-0.02030.2516-0.0586-0.06060.195-0.01330.217956.000223.409445.1975
31.5184-0.88751.10421.3582-0.14121.50670.029-0.48540.26220.31520.12210.3054-0.1831-0.53540.03720.23240.03750.09090.306-0.03330.1941.417326.420943.2683
41.0427-0.72940.57831.19140.20561.27850.03150.39160.2234-0.1912-0.06190.3894-0.0069-0.2517-0.02360.24430.0464-0.02010.30810.03960.252542.141626.150622.7491
50.7966-0.01120.28150.5408-0.23890.76840.21320.2903-0.4103-0.1546-0.2147-0.25880.33990.17610.02520.23520.06120.0170.2038-0.03440.218153.293917.621728.0497
61.6284-0.03950.91341.6455-0.22021.85070.40120.1827-0.3625-0.3223-0.13760.0630.5925-0.09060.40660.30880.0099-0.06140.1940.02640.387750.833310.582933.3362
71.68080.08620.13220.26430.04280.94350.35640.12690.48810.0664-0.1441-0.2917-0.5703-0.0014-0.03040.3835-0.00420.07470.2278-0.02670.53577.477441.65817.349
81.21210.5646-0.04942.02570.38551.90650.24250.55260.0266-0.5867-0.1656-0.31840.09470.37040.09650.33980.10860.07380.38640.05620.206182.447126.0282.7904
92.26440.2032-0.08382.2536-0.5651.1523-0.0763-0.21560.31130.2228-0.0943-0.70660.04140.2401-0.03460.1885-0.03720.00740.30130.01930.316787.137528.877120.9668
100.88280.25280.38160.9316-0.54640.79360.3345-0.0616-0.412-0.062-0.14970.150.4977-0.06930.060.35020.0197-0.08820.2394-0.00740.230678.499116.181714.5259
111.92182.6643-0.82733.9438-0.91310.5841-0.32830.0416-0.118-0.006-0.28860.29920.0712-0.4085-0.00390.3427-0.0752-0.03740.33230.00450.364741.134716.962433.5105
126.6014-7.7235-2.36159.13162.54441.35040.0353-0.10070.059-0.09390.0853-0.02220.10750.0453-0.02190.35540.0641-0.01020.3038-0.00560.417990.473218.663114.3921
130.32580.1349-0.17480.1261-0.10210.2569-0.0504-0.0255-0.02820.013-0.01990.0585-0.0126-0.0072-0.00110.457-0.09580.16010.8741-0.26030.775730.49440.725426.1754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 169:181 )A169 - 181
2X-RAY DIFFRACTION2( CHAIN A AND RESID 182:254 )A182 - 254
3X-RAY DIFFRACTION3( CHAIN A AND RESID 255:317 )A255 - 317
4X-RAY DIFFRACTION4( CHAIN A AND RESID 318:374 )A318 - 374
5X-RAY DIFFRACTION5( CHAIN A AND RESID 375:406 )A375 - 406
6X-RAY DIFFRACTION6( CHAIN A AND RESID 407:429 )A407 - 429
7X-RAY DIFFRACTION7( CHAIN B AND RESID 169:181 )B169 - 181
8X-RAY DIFFRACTION8( CHAIN B AND RESID 182:294 )B182 - 294
9X-RAY DIFFRACTION9( CHAIN B AND RESID 295:374 )B295 - 374
10X-RAY DIFFRACTION10( CHAIN B AND RESID 375:426 )B375 - 426
11X-RAY DIFFRACTION11( CHAIN A AND RESID 509:509 )A509
12X-RAY DIFFRACTION12( CHAIN B AND RESID 502:502 )B502
13X-RAY DIFFRACTION13( CHAIN A AND RESID 501:501 )A501

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