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- PDB-2c40: CRYSTAL STRUCTURE OF INOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROL... -

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Basic information

Entry
Database: PDB / ID: 2c40
TitleCRYSTAL STRUCTURE OF INOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROLASE FROM BACILLUS ANTHRACIS AT 2.2A RESOLUTION
ComponentsINOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROLASE FAMILY PROTEIN
KeywordsHYDROLASE / NUCLEOSIDE HYDROLASE / SPINE
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / metabolic process / metal ion binding
Similarity search - Function
Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
alpha-D-ribofuranose / Inosine-uridine preferring nucleoside hydrolase family protein
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMoroz, O.V. / Blagova, E.V. / Fogg, M.J. / Levdikov, V.M. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
CitationJournal: To be Published
Title: Crystal Structure of Inosine-Uridine Preferring Nucleoside Hydrolase from Bacillus Anthracis at 2.2A Resolution
Authors: Moroz, O.V. / Blagova, E.V. / Fogg, M.J. / Levdikov, V.M. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionOct 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROLASE FAMILY PROTEIN
B: INOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROLASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9136
Polymers70,5322
Non-polymers3804
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.154, 78.154, 203.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 312
2113B1 - 312

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Components

#1: Protein INOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROLASE FAMILY PROTEIN


Mass: 35266.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81QM4, purine nucleosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.6 Å3/Da / Density % sol: 51.5 %
Crystal growpH: 8.5 / Details: 22% PEG 3350, 0.2 M NACL, TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.2→24.81 Å / Num. obs: 37372 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.02 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HOZ

1hoz


Resolution: 2.2→67.88 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.306 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1867 5 %RANDOM
Rwork0.205 ---
obs0.207 35505 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→67.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 20 125 4836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224867
X-RAY DIFFRACTIONr_bond_other_d0.0020.024421
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9476653
X-RAY DIFFRACTIONr_angle_other_deg1.004310205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69623.555211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9115748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1491528
X-RAY DIFFRACTIONr_chiral_restr0.120.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025422
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021000
X-RAY DIFFRACTIONr_nbd_refined0.2150.21117
X-RAY DIFFRACTIONr_nbd_other0.190.24766
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22367
X-RAY DIFFRACTIONr_nbtor_other0.0950.22879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2118
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6551.53109
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06824896
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94132034
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7894.51757
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1747tight positional0.060.05
2689loose positional0.465
1747tight thermal0.160.5
2689loose thermal1.1110
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 115
Rwork0.259 2584
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)
11.62770.36390.09691.2797-0.27361.45510.0392-0.267-0.18990.0683-0.1164-0.0544-0.0264-0.12450.0772-0.06180.0418-0.1274-0.14020.0243-0.161915.7654-28.5839-10.5477
22.5081-0.09290.07151.7502-0.59222.38510.0291-0.1480.0478-0.1184-0.11120.3773-0.247-0.42080.0821-0.08860.1793-0.1946-0.0642-0.1864-0.0137-14.9849-21.2539-36.1009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 310
2X-RAY DIFFRACTION2B1 - 310

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