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- PDB-3shd: Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherich... -

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Entry
Database: PDB / ID: 3shd
TitleCrystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1
ComponentsPhosphatase nudJ
KeywordsHYDROLASE / Nudix fold / Nudix motif / (d)NDP/(d)NTP binding / dephosphorylation
Function / homology
Function and homology information


thiamine diphosphate phosphatase activity / nucleoside diphosphate phosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribonucleoside triphosphate phosphatase activity
Similarity search - Function
Phosphatase NudJ / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Phosphatase NudJ / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Phosphatase NudJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHong, M.K. / Kim, J.K. / Kang, L.W.
CitationJournal: To be Published
Title: Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli
Authors: Hong, M.K.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_auth_seq_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_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: Phosphatase nudJ
B: Phosphatase nudJ
C: Phosphatase nudJ
D: Phosphatase nudJ
E: Phosphatase nudJ
F: Phosphatase nudJ
G: Phosphatase nudJ
H: Phosphatase nudJ
I: Phosphatase nudJ
J: Phosphatase nudJ
K: Phosphatase nudJ
L: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,18772
Polymers209,41012
Non-polymers4,77760
Water5,134285
1
A: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8496
Polymers17,4511
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
A: Phosphatase nudJ
I: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-169 kcal/mol
Surface area13320 Å2
MethodPISA
14
B: Phosphatase nudJ
L: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-174 kcal/mol
Surface area13290 Å2
MethodPISA
15
C: Phosphatase nudJ
G: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-170 kcal/mol
Surface area13040 Å2
MethodPISA
16
D: Phosphatase nudJ
E: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-171 kcal/mol
Surface area13210 Å2
MethodPISA
17
F: Phosphatase nudJ
K: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-170 kcal/mol
Surface area13190 Å2
MethodPISA
18
H: Phosphatase nudJ
hetero molecules

J: Phosphatase nudJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z+1/41
Buried area5390 Å2
ΔGint-172 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.126, 111.126, 247.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Phosphatase nudJ


Mass: 17450.854 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O1:K1 / APEC / Gene: nudJ, Ecok1_10240, APECO1_216 / Production host: Escherichia coli (E. coli)
References: UniProt: A1AA28, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.65 Å3/Da / Density % sol: 66.26 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.4M ammonium sulfate, 0.1M MES buffer pH 6.0, 100mM MnCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 182291 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→50 Å / % possible all: 90.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.867 / SU B: 11.797 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29147 4943 5 %RANDOM
Rwork0.22638 ---
obs0.22967 93734 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14496 0 204 285 14985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02215060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.791.94320532
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62551788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49824.355744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.737152412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2931584
X-RAY DIFFRACTIONr_chiral_restr0.120.22184
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111580
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8261.59036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.551214652
X-RAY DIFFRACTIONr_scbond_it1.99236024
X-RAY DIFFRACTIONr_scangle_it3.2894.55880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 346 -
Rwork0.312 6491 -
obs--90.42 %

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