[English] 日本語
Yorodumi
- PDB-4nfx: Structure and atypical hydrolysis mechanism of the Nudix hydrolas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nfx
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 / phosphatase
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: 2.69 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
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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


Theoretical massNumber of molelcules
Total (without water)139,6078
Polymers139,6078
Non-polymers00
Water3,639202
1
A: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)17,4511
Polymers17,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)17,4511
Polymers17,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)17,4511
Polymers17,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)17,4511
Polymers17,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)17,4511
Polymers17,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)17,4511
Polymers17,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)17,4511
Polymers17,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)17,4511
Polymers17,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Putative Nudix hydrolase ymfB
B: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)34,9022
Polymers34,9022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-28 kcal/mol
Surface area14120 Å2
MethodPISA
10
C: Putative Nudix hydrolase ymfB
D: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)34,9022
Polymers34,9022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-29 kcal/mol
Surface area14300 Å2
MethodPISA
11
E: Putative Nudix hydrolase ymfB
F: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)34,9022
Polymers34,9022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-28 kcal/mol
Surface area14390 Å2
MethodPISA
12
G: Putative Nudix hydrolase ymfB
H: Putative Nudix hydrolase ymfB


Theoretical massNumber of molelcules
Total (without water)34,9022
Polymers34,9022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-25 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.960, 70.521, 145.031
Angle α, β, γ (deg.)90.00, 103.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative Nudix hydrolase ymfB


Mass: 17450.854 Da / Num. of mol.: 8
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium citrate buffer pH 4.0, 3.5%(w/v) PEG4000, 64mM magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 283K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.96405 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96405 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 40006 / % possible obs: 99.7 % / Observed criterion σ(F): 76.8 / Observed criterion σ(I): 3.1
Reflection shellResolution: 2.64→50 Å / % possible all: 99.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→33.56 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.841 / SU B: 15.229 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28807 1865 5 %RANDOM
Rwork0.2334 ---
obs0.23617 35479 98.21 %-
all-40006 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.004 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.04 Å2
2--0 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.69→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9703 0 0 202 9905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0199979
X-RAY DIFFRACTIONr_bond_other_d0.0010.029273
X-RAY DIFFRACTIONr_angle_refined_deg0.8811.93213593
X-RAY DIFFRACTIONr_angle_other_deg0.671321364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43851201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84324.372494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.215151612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3631556
X-RAY DIFFRACTIONr_chiral_restr0.0530.21469
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022359
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: 2.69→2.759 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 108 -
Rwork0.321 2497 -
obs--93.37 %
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)
10.3819-0.0510.17820.0451-0.17410.7997-0.02890.02660.0090.01020.0006-0.01720.0029-0.05460.02830.0492-0.0062-0.00450.02620.00180.049314.1342.55330.797
20.07060.0013-0.01620.23090.15861.2083-0.0178-0.02950.0024-0.0221-0.0029-0.04290.0367-0.03780.02070.0193-0.00040.01470.02350.00750.056415.6511.12858.769
30.06380.00440.12830.0543-0.06770.676-0.0126-0.031-0.01610.0154-0.0222-0.02130.0088-0.03060.03480.0191-0.00520.00740.04570.00410.055721.51834.81748.022
40.299-0.02830.05450.0619-0.12040.94780.0060.0019-0.02520.0157-0.0257-0.0278-0.0631-0.05660.01970.02260.00990.0040.04340.00790.063121.86536.32419.864
50.196-0.16920.04490.173-0.02230.8093-0.011-0.0450.0249-0.00110.0038-0.0285-0.0327-0.05340.00730.00540.0165-0.00540.0567-0.01060.0725-14.16338.0653.431
60.39280.1832-0.02730.2602-0.18320.8015-0.0160.0871-0.0058-0.00710.0240.03590.01660.0298-0.00810.01190.01560.00070.05460.00250.0535-14.08641.52231.18
70.4355-0.0648-0.02640.1244-0.05961.0753-0.01360.03360.023-0.007-0.07460.0060.0602-0.09840.08830.004-0.00310.00560.063-0.02740.0705-22.38412.57876.264
80.22690.2592-0.16840.3137-0.21920.9168-0.010.003-0.002-0.0254-0.0281-0.01830.04980.06810.03820.01630.02510.02590.05490.02010.0712-24.24214.13147.676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 153
2X-RAY DIFFRACTION1A201 - 233
3X-RAY DIFFRACTION2B1 - 149
4X-RAY DIFFRACTION2B201 - 220
5X-RAY DIFFRACTION3C1 - 153
6X-RAY DIFFRACTION3C201 - 217
7X-RAY DIFFRACTION4D1 - 150
8X-RAY DIFFRACTION4D201 - 223
9X-RAY DIFFRACTION5E1 - 153
10X-RAY DIFFRACTION5E201 - 231
11X-RAY DIFFRACTION6F1 - 153
12X-RAY DIFFRACTION6F201 - 231
13X-RAY DIFFRACTION7G1 - 153
14X-RAY DIFFRACTION7G201 - 218
15X-RAY DIFFRACTION8H1 - 145
16X-RAY DIFFRACTION8H201 - 228

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more