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Entry
Database: PDB / ID: 4nfw
TitleStructure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli
ComponentsPutative Nudix hydrolase ymfB
KeywordsHYDROLASE / Nudix hydrolase / YmfB / Nucleoside triphosphatase / Metal ions-based catalysis / Nudix motif / phophatase
Function / homologyNucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Alpha-Beta Complex / Alpha Beta / : / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHong, M.K. / Kim, J.K. / Kang, L.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli
Authors: Hong, M.K. / Ribeiro, A.J.M. / Kim, J.K. / Ngo, H.P.T. / Kim, J. / Lee, C.H. / Ahn, Y.J. / Fernandes, P.A. / Li, Q. / Ramos, M.J. / Kang, L.W.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Nudix hydrolase ymfB
B: Putative Nudix hydrolase ymfB
C: Putative Nudix hydrolase ymfB
D: Putative Nudix hydrolase ymfB
E: Putative Nudix hydrolase ymfB
F: Putative Nudix hydrolase ymfB
G: Putative Nudix hydrolase ymfB
H: Putative Nudix hydrolase ymfB
I: Putative Nudix hydrolase ymfB
J: Putative Nudix hydrolase ymfB
K: Putative Nudix hydrolase ymfB
L: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,98169
Polymers209,41012
Non-polymers4,57157
Water6,017334
1
A: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6984
Polymers17,4511
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
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: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7945
Polymers17,4511
Non-polymers3434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
A: Putative Nudix hydrolase ymfB
I: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,54710
Polymers34,9022
Non-polymers6458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area13330 Å2
MethodPISA
14
B: Putative Nudix hydrolase ymfB
L: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,64311
Polymers34,9022
Non-polymers7419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-25 kcal/mol
Surface area13490 Å2
MethodPISA
15
C: Putative Nudix hydrolase ymfB
G: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-24 kcal/mol
Surface area13610 Å2
MethodPISA
16
D: Putative Nudix hydrolase ymfB
E: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-28 kcal/mol
Surface area13740 Å2
MethodPISA
17
F: Putative Nudix hydrolase ymfB
K: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-26 kcal/mol
Surface area14060 Å2
MethodPISA
18
H: Putative Nudix hydrolase ymfB
J: Putative Nudix hydrolase ymfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69812
Polymers34,9022
Non-polymers79610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-27 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.387, 111.387, 247.489
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
Putative Nudix hydrolase ymfB


Mass: 17450.854 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 'clone D i14' / Gene: i14_1356 / Production host: Escherichia coli (E. coli) / References: UniProt: G7RNP0
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mn
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.67 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.4M ammonium sulfate, 0.1M MES buffer pH 6.0, 0.1M 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: 0.97198 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97198 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 128765 / % possible obs: 96.8 % / Observed criterion σ(F): 72.3 / Observed criterion σ(I): 9
Reflection shellResolution: 2.3→50 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→32.42 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.871 / SU B: 9.423 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 6505 5.1 %RANDOM
Rwork0.24024 ---
obs0.24273 122247 96.83 %-
all-128765 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0 Å2-0 Å2
2--0.7 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14375 0 197 334 14906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01914931
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213719
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.94220351
X-RAY DIFFRACTIONr_angle_other_deg0.886331608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03951768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22424.301737
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.724152388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4621584
X-RAY DIFFRACTIONr_chiral_restr0.0960.22200
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023516
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 484 -
Rwork0.373 8689 -
obs--93.17 %

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