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- PDB-4zg5: Structural and functional insights into Survival endonuclease, an... -

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Basic information

Entry
Database: PDB / ID: 4zg5
TitleStructural and functional insights into Survival endonuclease, an important virulence factor of Brucella abortus
Components5'-nucleotidase SurE
KeywordsHYDROLASE
Function / homology
Function and homology information


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
5'-nucleotidase SurE
Similarity search - Component
Biological speciesBrucella abortus S19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTarique, K.F. / Abdul Rehman, S.A. / Devi, S. / Gourinath, S.
Funding support India, 3items
OrganizationGrant numberCountry
CSIR India
DBT India
ICMR India
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structural and functional insights into the stationary-phase survival protein SurE, an important virulence factor of Brucella abortus
Authors: Tarique, K.F. / Abdul Rehman, S.A. / Devi, S. / Tomar, P. / Gourinath, S.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 6, 2015ID: 4QEA
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-nucleotidase SurE
A: 5'-nucleotidase SurE
C: 5'-nucleotidase SurE
G: 5'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5558
Polymers114,4584
Non-polymers974
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-119 kcal/mol
Surface area37370 Å2
Unit cell
Length a, b, c (Å)50.181, 121.068, 82.431
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22C
13D
23G
14A
24C
15A
25G
16C
26G

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALADA1 - 2501 - 250
21ALAALAAB1 - 2501 - 250
12GLYGLYDA1 - 2481 - 248
22GLYGLYCC1 - 2481 - 248
13GLYGLYDA1 - 2521 - 252
23GLYGLYGD1 - 2521 - 252
14ALAALAAB1 - 2491 - 249
24ALAALACC1 - 2491 - 249
15ALAALAAB1 - 2501 - 250
25ALAALAGD1 - 2501 - 250
16ALAALACC1 - 2491 - 249
26ALAALAGD1 - 2491 - 249

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
5'-nucleotidase SurE / Survival endonuclease / Nucleoside 5'-monophosphate phosphohydrolase


Mass: 28614.494 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus S19 (bacteria) / Strain: S19 / Gene: surE, BAbS19_I08450 / Production host: Escherichia coli (E. coli) / References: UniProt: B2S5B9, 5'-nucleotidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15% PEG 4000, TRIS, 0.2M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 75815 / % possible obs: 97.8 % / Redundancy: 3.3 % / Net I/σ(I): 21.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.16 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TY2

3ty2


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.682 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22725 3807 5 %RANDOM
Rwork0.19841 ---
obs0.19986 71978 97.66 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.94 Å2
2--3.64 Å20 Å2
3----3.72 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7477 0 4 215 7696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197650
X-RAY DIFFRACTIONr_bond_other_d0.010.027299
X-RAY DIFFRACTIONr_angle_refined_deg2.0821.96510375
X-RAY DIFFRACTIONr_angle_other_deg1.581316715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4765989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82823.07329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.682151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1031571
X-RAY DIFFRACTIONr_chiral_restr0.150.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218728
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021697
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6872.6223974
X-RAY DIFFRACTIONr_mcbond_other2.6872.6213973
X-RAY DIFFRACTIONr_mcangle_it3.7053.9174957
X-RAY DIFFRACTIONr_mcangle_other3.7053.9174958
X-RAY DIFFRACTIONr_scbond_it3.863.0153676
X-RAY DIFFRACTIONr_scbond_other3.8613.0163665
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.564.3625419
X-RAY DIFFRACTIONr_long_range_B_refined7.12921.4918426
X-RAY DIFFRACTIONr_long_range_B_other7.11221.48377
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D144730.07
12A144730.07
21D144340.09
22C144340.09
31D142350.09
32G142350.09
41A143000.08
42C143000.08
51A142130.09
52G142130.09
61C142000.09
62G142000.09
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 284 -
Rwork0.298 5312 -
obs--97.47 %
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)
11.11960.25730.04140.96150.08691.51440.0672-0.09420.09450.18350.00290.033-0.043-0.0456-0.070.05430.00670.04070.01210.00550.06593.677-3.9316.906
21.0406-0.214-0.06171.28770.10712.363-0.02290.14270.0393-0.2139-0.0051-0.0445-0.26290.27390.02810.0799-0.05110.02110.0687-0.00280.0533-8.259-0.882-31.682
30.8559-0.07630.39391.2579-0.42421.43160.034-0.075-0.10240.07330.0089-0.03270.11730.0517-0.0430.03970.00980.02270.01380.01450.08482.114-27.9375.307
40.7789-0.2065-0.08321.2390.34081.59950.00890.109-0.2234-0.156-0.00080.23440.1923-0.1628-0.0080.079-0.02520.00720.0433-0.00930.1866-16.313-23.483-31.088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 252
2X-RAY DIFFRACTION2A1 - 250
3X-RAY DIFFRACTION3C1 - 249
4X-RAY DIFFRACTION4G1 - 252

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