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- PDB-2wqk: Crystal Structure of Sure Protein from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 2wqk
TitleCrystal Structure of Sure Protein from Aquifex aeolicus
Components5'-NUCLEOTIDASE SURE
KeywordsHYDROLASE / SURE PROTEIN / PUTATIVE ACID PHOSPHATASE / STRUCTURAL GENOMICS / 3-D STRUCTURE / MIXED ALPHA/BETA PROTEIN / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


3'-nucleotidase activity / exopolyphosphatase 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
5'-nucleotidase SurE
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAntonyuk, S.V. / Ellis, M.J. / Strange, R.W. / Hasnain, S.S. / Bessho, Y. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of Sure Protein from Aquifex Aeolicus Vf5 at 1.5 A Resolution.
Authors: Antonyuk, S.V. / Ellis, M.J. / Strange, R.W. / Bessho, Y. / Kuramitsu, S. / Shinkai, A. / Yokoyama, S. / Hasnain, S.S.
History
DepositionAug 23, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionSep 29, 2009ID: 2PHJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4Dec 20, 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 / struct_site
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 / _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: 5'-NUCLEOTIDASE SURE
B: 5'-NUCLEOTIDASE SURE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6336
Polymers56,3942
Non-polymers2384
Water10,899605
1
A: 5'-NUCLEOTIDASE SURE
B: 5'-NUCLEOTIDASE SURE
hetero molecules

A: 5'-NUCLEOTIDASE SURE
B: 5'-NUCLEOTIDASE SURE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,26512
Polymers112,7894
Non-polymers4768
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area18640 Å2
ΔGint-241.45 kcal/mol
Surface area37590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.006, 65.006, 239.194
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 5'-NUCLEOTIDASE SURE / NUCLEOSIDE 5'-MONOPHOSPHATE PHOSPHOHYDROLASE


Mass: 28197.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Strain: VF5 / Gene: SURE, AQ_832 / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: O67004, 5'-nucleotidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.59 Å3/Da / Density % sol: 52.43 % / Description: NONE
Crystal growMethod: microbatch / pH: 4.5
Details: 2.5 M NACL, 0.1 M ACETATE PH 4.5, 0.2 M LI SULFATE, OIL (TERA), MICROBATCH UNDER OIL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 27, 2007 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.5→36.5 Å / Num. obs: 91484 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3 / % possible all: 68.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J9L

1j9l


Resolution: 1.5→36.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.114 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19085 4577 5 %RANDOM
Rwork0.15573 ---
obs0.15746 86861 96.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 12 605 4549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224246
X-RAY DIFFRACTIONr_bond_other_d0.0020.022948
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9755796
X-RAY DIFFRACTIONr_angle_other_deg1.01937206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1195548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39823.838198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97815745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8391530
X-RAY DIFFRACTIONr_chiral_restr0.1080.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024754
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02878
X-RAY DIFFRACTIONr_nbd_refined0.2370.2788
X-RAY DIFFRACTIONr_nbd_other0.1940.23038
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22054
X-RAY DIFFRACTIONr_nbtor_other0.0850.22138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2382
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5931.52564
X-RAY DIFFRACTIONr_mcbond_other0.8211.51047
X-RAY DIFFRACTIONr_mcangle_it2.41624192
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.20431739
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.524.51581
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.55837504
X-RAY DIFFRACTIONr_sphericity_free7.9733607
X-RAY DIFFRACTIONr_sphericity_bonded4.65137076
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 223 -
Rwork0.255 4163 -
obs--68.2 %

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