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- PDB-2v4o: Crystal structure of Salmonella typhimurium SurE at 2.75 angstrom... -

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Basic information

Entry
Database: PDB / ID: 2v4o
TitleCrystal structure of Salmonella typhimurium SurE at 2.75 angstrom resolution in monoclinic form
ComponentsMULTIFUNCTIONAL PROTEIN SUR EMulti-function printer
KeywordsHYDROLASE / MONONUCLEOTIDASE / SURVIVAL PROTEIN / STATIONARY PHASE / SUR E / PHOSPHATASE / DIVALENT METAL ION / NUCLEOTIDE-BINDING / MULTIFUNCTIONAL ENZYME / ROSSMANN FOLD / METAL-BINDING / DOMAIN SWAPPING
Function / homology
Function and homology information


3'-nucleotidase / 3'-nucleotidase activity / exopolyphosphatase / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Stationary-phase Survival Protein Sure Homolog; Chain: A, / Survival protein SurE-like phosphatase/nucleotidase / Survival protein SurE / Survival protein SurE-like phosphatase/nucleotidase / SurE-like phosphatase/nucleotidase superfamily / Survival protein SurE / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 5'/3'-nucleotidase SurE
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsAnju, P. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: FEBS J. / Year: 2008
Title: Structural and Functional Studies on a Mesophilic Stationary Phase Survival Protein (Sur E) from Salmonella Typhimurium
Authors: Pappachan, A. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionSep 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MULTIFUNCTIONAL PROTEIN SUR E
B: MULTIFUNCTIONAL PROTEIN SUR E
C: MULTIFUNCTIONAL PROTEIN SUR E
D: MULTIFUNCTIONAL PROTEIN SUR E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,84011
Polymers114,4604
Non-polymers3797
Water1,33374
1
A: MULTIFUNCTIONAL PROTEIN SUR E
B: MULTIFUNCTIONAL PROTEIN SUR E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3745
Polymers57,2302
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-71.7 kcal/mol
Surface area25360 Å2
MethodPQS
2
C: MULTIFUNCTIONAL PROTEIN SUR E
D: MULTIFUNCTIONAL PROTEIN SUR E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4666
Polymers57,2302
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-82.1 kcal/mol
Surface area25590 Å2
MethodPQS
Unit cell
Length a, b, c (Å)161.081, 95.299, 94.572
Angle α, β, γ (deg.)90.00, 98.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MULTIFUNCTIONAL PROTEIN SUR E / Multi-function printer / 5'/3'-NUCLEOTIDASE / SURVIVAL PROTEIN / NUCLEOSIDE MONOPHOSPHATE PHOSPHOHYDROLASE / EXOPOLYPHOSPHATASE


Mass: 28615.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: LT2 / Plasmid: PSBET-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase, fructose-bisphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.1 Å3/Da / Density % sol: 60.2 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES (PH 6.5) AND 12% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 37552 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.32 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J9J

1j9j


Resolution: 2.71→93.25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 23.928 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.66 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25428 1884 5 %RANDOM
Rwork0.18952 ---
obs0.19271 35604 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å2-0.29 Å2
2---0.56 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.71→93.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 20 74 7636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217760
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.96110627
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7651016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67223.825332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.952151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6581558
X-RAY DIFFRACTIONr_chiral_restr0.1220.21226
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.23391
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.25207
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6941.55163
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23728166
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93232890
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1174.52461
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.714→2.784 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.389 110
Rwork0.316 2033
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)
11.52810.0202-0.03830.9288-0.16641.61420.0918-0.061-0.14320.1275-0.09520.17080.0878-0.13290.0034-0.103-0.08460.0062-0.00930.0297-0.068991.164542.626625.7432
21.4979-0.1344-0.02541.1321-0.16471.52970.0813-0.339-0.01470.36430.01550.0032-0.20960.0365-0.0968-0.0121-0.05560.02890.02720.0083-0.2128100.317352.525840.6806
30.8540.43590.01441.4002-0.01870.62270.0203-0.1045-0.13460.1445-0.0535-0.3521-0.09830.1120.0332-0.0643-0.01520.0093-0.11950.0291-0.0126129.914464.069813.3912
40.81250.14290.23931.20210.32281.14620.00780.0368-0.0348-0.1353-0.0083-0.0391-0.06410.04320.0005-0.0249-0.00660.0348-0.1443-0.0074-0.0838117.227358.8184-1.94
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 253
2X-RAY DIFFRACTION2B0 - 253
3X-RAY DIFFRACTION3C0 - 253
4X-RAY DIFFRACTION4D-4 - 253

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