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- PDB-3mkm: Crystal structure of the E. coli pyrimidine nucleoside hydrolase ... -

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Basic information

Entry
Database: PDB / ID: 3mkm
TitleCrystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)
ComponentsPutative uncharacterized protein YeiK
KeywordsHYDROLASE / PYRIMIDINE NUCLEOSIDE HYDROLASE / BACTERIAL NUCLEOSIDASE / NUCLEOTIDE METABOLISM / METALLOENZYME
Function / homology
Function and homology information


ribosylpyrimidine nucleosidase / pyrimidine ribonucleoside catabolic process / uridine nucleosidase activity / pyrimidine nucleobase metabolic process / calcium ion binding
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
Pyrimidine-specific ribonucleoside hydrolase RihB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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.
#2: Journal: Biochemistry / Year: 2006
Title: New insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product
Authors: Muzzolini, L. / Versees, W. / Tornaghi, P. / Van Holsbeke, E. / Steyaert, J. / Degano, M.
#3: Journal: Biochemistry / Year: 1998
Title: Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor
Authors: Degano, M. / Almo, S.C. / Sacchettini, J.C. / Schramm, V.L.
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)136,3378
Polymers136,1774
Non-polymers1604
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-47 kcal/mol
Surface area42320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.601, 85.231, 90.060
Angle α, β, γ (deg.)66.65, 79.39, 85.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 12
2111B1 - 12
3111C1 - 12
4111D1 - 12
1216A13 - 15
2216B13 - 15
3216C13 - 15
4216D13 - 15
1311A16 - 73
2311B16 - 73
3311C16 - 73
4311D16 - 73
1416A74 - 85
2416B74 - 85
3416C74 - 85
4416D74 - 85
1514A86 - 97
2514B86 - 97
3514C86 - 97
4514D86 - 97
1611A98 - 194
2611B98 - 194
3611C98 - 194
4611D98 - 194
1714A195 - 222
2714B195 - 222
3714C195 - 222
4714D195 - 222
1816A223 - 236
2816B223 - 236
3816C223 - 236
4816D223 - 236
1911A237 - 279
2911B237 - 279
3911C237 - 279
4911D237 - 279
11014A280
21014B280
31014C280
41014D280
11111A281 - 305
21111B281 - 305
31111C281 - 305
41111D281 - 305
11214A305 - 312
21214B305 - 312
31214C305 - 312
41214D305 - 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.1M TRIS PH 8.5, 0.2M SODIUM CHLORIDE, 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
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→81.65 Å / Num. obs: 58257 / % possible obs: 94.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.363 / % possible all: 94.5

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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: YEIK PDB CODE 1Q8F

1q8f


Resolution: 2.2→47.91 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.522 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22284 2954 5.1 %RANDOM
Rwork0.18494 ---
obs0.18687 55302 94.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.962 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.59 Å21.31 Å2
2---1.2 Å20.04 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9129 0 4 527 9660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229350
X-RAY DIFFRACTIONr_bond_other_d0.0020.026130
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.97612732
X-RAY DIFFRACTIONr_angle_other_deg1.101315139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1151211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86225.389373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.953151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7231540
X-RAY DIFFRACTIONr_chiral_restr0.0810.21499
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021664
X-RAY DIFFRACTIONr_nbd_refined0.2040.21903
X-RAY DIFFRACTIONr_nbd_other0.1870.26173
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24554
X-RAY DIFFRACTIONr_nbtor_other0.0860.24514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.070.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4571.56298
X-RAY DIFFRACTIONr_mcbond_other0.1291.52472
X-RAY DIFFRACTIONr_mcangle_it0.69629820
X-RAY DIFFRACTIONr_scbond_it1.26733509
X-RAY DIFFRACTIONr_scangle_it1.8164.52912
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
1A2874tight positional0.050.05
2B2874tight positional0.050.05
3C2874tight positional0.040.05
4D2874tight positional0.040.05
1A611medium positional0.70.5
2B611medium positional0.780.5
3C611medium positional0.690.5
4D611medium positional0.550.5
1A148loose positional0.985
2B148loose positional1.545
3C148loose positional0.655
4D148loose positional0.885
1A2874tight thermal0.10.5
2B2874tight thermal0.10.5
3C2874tight thermal0.090.5
4D2874tight thermal0.090.5
1A611medium thermal0.872
2B611medium thermal0.752
3C611medium thermal0.72
4D611medium thermal0.442
1A148loose thermal4.7610
2B148loose thermal2.9110
3C148loose thermal4.2610
4D148loose thermal1.6210
LS refinement shellResolution: 2.204→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 176 -
Rwork0.231 3807 -
obs--88.71 %
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)
10.7016-0.2345-0.28251.188-0.00790.9162-0.0196-0.09550.04010.08290.0543-0.004-0.1009-0.0483-0.0347-0.08230.0306-0.0477-0.0729-0.015-0.1282-10.150720.652818.3655
21.09740.232-0.42381.46230.13051.3135-0.00260.08110.0969-0.19370.0408-0.1867-0.08480.1254-0.0381-0.0761-0.0052-0.0231-0.08840.0128-0.0758.66922.6096-17.3801
30.703-0.6045-0.33552.3675-0.58591.7105-0.1577-0.2357-0.08070.26530.110.00420.24430.01060.04780.0168-0.00490.0207-0.04930.0231-0.0443-3.2478-22.459218.9434
40.54760.1006-0.20390.89550.09561.9866-0.0620.1209-0.063-0.16050.0140.05230.3478-0.10340.0480.0866-0.01780.0252-0.0884-0.0152-0.06553.941-20.5027-20.3959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 311
2X-RAY DIFFRACTION2B2 - 311
3X-RAY DIFFRACTION3C3 - 311
4X-RAY DIFFRACTION4D3 - 311

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