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- PDB-6ba0: Pyrimidine-specific Ribonucleoside Hydrolase from Gardnerella vag... -

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Basic information

Entry
Database: PDB / ID: 6ba0
TitlePyrimidine-specific Ribonucleoside Hydrolase from Gardnerella vaginalis
ComponentsCytidine/uridine-specific hydrolase
KeywordsHYDROLASE / Nucleoside hydrolase / Nitrogen metabolism
Function / homology
Function and homology information


Hydrolases; Glycosylases / hydrolase activity, acting on glycosyl bonds / metabolic process
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
Cytidine/uridine-specific hydrolase
Similarity search - Component
Biological speciesGardnerella vaginalis 315-A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsRenner, N. / Jacques, D.A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1036521 Australia
CitationJournal: To Be Published
Title: Pyrimidine-specific Ribonucleoside Hydrolase RihB from Gardnerella vaginalis
Authors: Renner, N. / Jacques, D.A.
History
DepositionOct 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
A: Cytidine/uridine-specific hydrolase
B: Cytidine/uridine-specific hydrolase
C: Cytidine/uridine-specific hydrolase
D: Cytidine/uridine-specific hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,18417
Polymers136,7044
Non-polymers47913
Water15,529862
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-137 kcal/mol
Surface area45470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.070, 79.360, 115.990
Angle α, β, γ (deg.)90.000, 99.620, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1 - 312 / Label seq-ID: 4 - 315

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cytidine/uridine-specific hydrolase


Mass: 34176.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gardnerella vaginalis 315-A (bacteria) / Gene: rihA, HMPREF9435_0920 / Plasmid: pOPTG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): C41 / References: UniProt: F5LUB1, Hydrolases; Glycosylases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M Sodium Acetate 0.2M Ammonium Sulfate 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.03→61.87 Å / Num. obs: 96089 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.079 / Rrim(I) all: 0.213 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.03-2.066.60.94247010.6480.3871.02199.2
11.12-61.876.10.0766260.9950.0320.08298.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.03 Å48.79 Å
Translation2.03 Å48.79 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Blu-Icedata collection
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.22data extraction
MOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MAS

1mas


Resolution: 2.03→61.87 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.209 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1741 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 4802 5 %RANDOM
Rwork0.1863 ---
obs0.1879 91261 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.43 Å2 / Biso mean: 19.57 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20.36 Å2
2---0.41 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.03→61.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9396 0 13 862 10271
Biso mean--34.89 23.9 -
Num. residues----1232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199604
X-RAY DIFFRACTIONr_bond_other_d0.0020.029002
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.96613132
X-RAY DIFFRACTIONr_angle_other_deg0.948320904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64251226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.19724.798396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.528151542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6451548
X-RAY DIFFRACTIONr_chiral_restr0.0790.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021742
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A198660.07
12B198660.07
21A194560.08
22C194560.08
31A193720.08
32D193720.08
41B196560.06
42C196560.06
51B196240.06
52D196240.06
61C197880.05
62D197880.05
LS refinement shellResolution: 2.03→2.083 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 377 -
Rwork0.253 6674 -
all-7051 -
obs--99.24 %

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