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- PDB-3mkn: Crystal structure of the E. coli pyrimidine nucleosidase YeiK bou... -

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Basic information

Entry
Database: PDB / ID: 3mkn
TitleCrystal structure of the E. coli pyrimidine nucleosidase YeiK bound to a competitive inhibitor
ComponentsPutative uncharacterized protein YeiK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Pyrimidine nucleoside hydrolase / nucleotide metabolism / enzyme-inhibitor complex / metalloenzyme / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


ribosylpyrimidine nucleosidase / pyrimidine ribonucleoside catabolic process / uridine nucleosidase activity / purine nucleosidase activity / pyrimidine nucleobase metabolic process / purine nucleoside catabolic process / calcium ion binding / cytosol
Similarity search - Function
Pyrimidine-specific ribonucleoside hydrolase RihB / Inosine/uridine-preferring nucleoside hydrolase, conserved site / Inosine-uridine preferring nucleoside hydrolase family signature. / 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
Chem-DNB / Pyrimidine-specific ribonucleoside hydrolase RihB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarau, G. / Fornili, A. / Giabbai, B. / Degano, M.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
Title: Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures
Authors: Fornili, A. / Giabbai, B. / Garau, G. / Degano, M.
#1: Journal: Structure / Year: 2004
Title: Crystal structure to 1.7 A of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy
Authors: Giabbai, B. / Degano, M.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein YeiK
B: Putative uncharacterized protein YeiK
C: Putative uncharacterized protein YeiK
D: Putative uncharacterized protein YeiK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,29412
Polymers136,1774
Non-polymers1,1178
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-47 kcal/mol
Surface area41170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.851, 86.446, 97.817
Angle α, β, γ (deg.)90.00, 98.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 78
2111B1 - 78
3111C1 - 78
4111D1 - 78
1216A79 - 85
2216B79 - 85
3216C79 - 85
4216D79 - 85
1314A86 - 97
2314B86 - 97
3314C86 - 97
4314D86 - 97
1411A98 - 194
2411B98 - 194
3411C98 - 194
4411D98 - 194
1516A212 - 222
2516B212 - 222
3516C212 - 222
4516D212 - 222
1616A223 - 236
2616B223 - 236
3616C223 - 236
4616D223 - 236
1711A237 - 305
2711B237 - 305
3711C237 - 305
4711D237 - 305
1814A306 - 312
2814B306 - 312
3814C306 - 312
4814D306 - 312

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Components

#1: Protein
Putative uncharacterized protein YeiK / pyrimidine nucleoside hydrolase / RihB


Mass: 34044.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: YeiK / Plasmid: pET28-YeiK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3T3U2, ribosylpyrimidine nucleosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-DNB / (2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol / Diaminophenyl iminoribitol


Mass: 239.271 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND 3,4-DIAMINOPHENYL-IMINORIBITOL (DAPIR) LABELED AS DNB IN THIS ENTRY CAN BEHAVIOR AS A ...THE LIGAND 3,4-DIAMINOPHENYL-IMINORIBITOL (DAPIR) LABELED AS DNB IN THIS ENTRY CAN BEHAVIOR AS A COMPETITIVE INHIBITOR OF THE E. COLI PYRIMIDINE-SPECIFIC NH YEIK.

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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: 52.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Bis-Tris pH 6.5, 45% PPG 500, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2005 / Details: Silicon crystal
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. all: 91924 / Num. obs: 91924 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.08 / Net I/σ(I): 10.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.465 / % possible all: 94.4

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q8F

1q8f


Resolution: 2→44.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.44 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19587 4601 5 %RANDOM
Rwork0.17412 ---
obs0.17523 87302 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.102 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20.55 Å2
2---0.04 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8988 0 72 588 9648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.98512660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0151190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50625.286367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.751151529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9951542
X-RAY DIFFRACTIONr_chiral_restr0.0940.21504
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.24690
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26499
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2716
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6591.56134
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05129685
X-RAY DIFFRACTIONr_scbond_it1.68533547
X-RAY DIFFRACTIONr_scangle_it2.7454.52975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1804tight positional0.040.05
2B1804tight positional0.060.05
3C1804tight positional0.040.05
4D1804tight positional0.050.05
1A121medium positional0.650.5
2B121medium positional0.470.5
3C121medium positional0.260.5
4D121medium positional0.240.5
1A93loose positional0.935
2B93loose positional0.615
3C93loose positional0.365
4D93loose positional0.315
1A1804tight thermal0.140.5
2B1804tight thermal0.190.5
3C1804tight thermal0.120.5
4D1804tight thermal0.160.5
1A121medium thermal0.832
2B121medium thermal0.882
3C121medium thermal0.482
4D121medium thermal0.912
1A93loose thermal3.4810
2B93loose thermal6.9910
3C93loose thermal2.3110
4D93loose thermal2.9210
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 339 -
Rwork0.229 6195 -
obs--93.76 %
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)
13.8640.1942-1.0431.22920.18481.68040.1812-1.19280.77530.22710.0883-0.134-0.23130.4577-0.2695-0.0041-0.0424-0.030.2292-0.27770.015332.874-0.67837.438
21.1226-0.3287-0.17361.04680.27270.6458-0.0081-0.0708-0.1823-0.00150.0231-0.07210.05670.0527-0.0151-0.14720.0031-0.0034-0.21030.0181-0.089439.517-28.1739.298
32.67070.41270.16641.45760.26721.41730.1225-0.91320.0570.4012-0.13480.3116-0.005-0.45560.01220.0010.01750.0970.29150.0011-0.0565-9.028-13.7238.505
42.2084-0.0210.15120.64030.1340.58690.03040.2653-0.3468-0.1204-0.01440.06030.0251-0.0613-0.016-0.1210.0062-0.0249-0.1409-0.0353-0.0133-3.339-30.3332.827
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 311
2X-RAY DIFFRACTION2B3 - 310
3X-RAY DIFFRACTION3C3 - 311
4X-RAY DIFFRACTION4D3 - 311

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