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- PDB-4kpo: Plant nucleoside hydrolase - ZmNRh3 enzyme -

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Basic information

Entry
Database: PDB / ID: 4kpo
TitlePlant nucleoside hydrolase - ZmNRh3 enzyme
ComponentsNucleoside N-ribohydrolase 3
KeywordsHYDROLASE / IU-NRHs
Function / homology
Function and homology information


hydrolase activity, hydrolyzing N-glycosyl compounds / organonitrogen compound metabolic process / nucleobase-containing compound metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / 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
Nucleoside N-ribohydrolase 3
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMorera, S. / Vigouroux, A. / Kopecny, D.
CitationJournal: Plant Physiol. / Year: 2013
Title: Structure and Function of Nucleoside Hydrolases from Physcomitrella patens and Maize Catalyzing the Hydrolysis of Purine, Pyrimidine, and Cytokinin Ribosides.
Authors: Kopecna, M. / Blaschke, H. / Kopecny, D. / Vigouroux, A. / Koncitikova, R. / Novak, O. / Kotland, O. / Strnad, M. / Morera, S. / von Schwartzenberg, K.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Nucleoside N-ribohydrolase 3
B: Nucleoside N-ribohydrolase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6624
Polymers71,5822
Non-polymers802
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-44 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.440, 85.780, 87.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoside N-ribohydrolase 3 / Pyrimidine-specific ribonucleoside hydrolase rihB


Mass: 35790.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: NRH3 / Production host: Escherichia coli (E. coli)
References: UniProt: B6T563, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM Tris-HCl, 150 mM NaCl, 20% PEG 2000 MME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2011
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.49→47.8 Å / Num. obs: 20483 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 64.74 Å2
Reflection shellResolution: 2.49→2.62 Å / % possible all: 91.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B9X

3b9x


Resolution: 2.49→43.69 Å / Cor.coef. Fo:Fc: 0.9344 / Cor.coef. Fo:Fc free: 0.8971 / SU R Cruickshank DPI: 1.176 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 1015 4.96 %RANDOM
Rwork0.2095 ---
obs0.2113 20483 98.89 %-
all-20050 --
Displacement parametersBiso mean: 70.25 Å2
Baniso -1Baniso -2Baniso -3
1-6.2758 Å20 Å20 Å2
2--14.3197 Å20 Å2
3----20.5954 Å2
Refine analyzeLuzzati coordinate error obs: 0.414 Å
Refinement stepCycle: LAST / Resolution: 2.49→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 2 30 4820
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084904HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.086686HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1617SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes705HARMONIC5
X-RAY DIFFRACTIONt_it4904HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion22.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion659SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5718SEMIHARMONIC4
LS refinement shellResolution: 2.49→2.62 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.27 128 4.67 %
Rwork0.2473 2614 -
all0.2483 2742 -
obs--98.89 %
Refinement TLS params.Method: refined / Origin x: 18.9615 Å / Origin y: -24.7575 Å / Origin z: -11.3169 Å
111213212223313233
T-0.1548 Å20.0298 Å2-0.0471 Å2--0.1301 Å2-0.0341 Å2---0.1197 Å2
L0.8871 °20.2966 °20.04 °2-3.3676 °20.3927 °2--0.4635 °2
S0.0277 Å °0.0758 Å °-0.1003 Å °-0.2426 Å °-0.0016 Å °-0.0944 Å °0.0102 Å °-0.0381 Å °-0.0261 Å °
Refinement TLS groupSelection details: { *|* }

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