[English] 日本語
Yorodumi
- PDB-3mpd: Crystal structure of nucleoside diphosphate kinase from encephali... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mpd
TitleCrystal structure of nucleoside diphosphate kinase from encephalitozoon cuniculi, cubic form, apo
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / SSGCID / NIH / NIAID / SBRI / UW / EMERALD BIOSTRUCTURES / ENCEPHALITOZOON CUNICULI / KINASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be published
Title: Crystal structure of nucleoside diphosphate kinase from encephalitozoon cuniculi
Authors: Gardberg, A. / Edwards, T.E. / Staker, B. / SSGCID
History
DepositionApr 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0233
Polymers33,9612
Non-polymers621
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-15 kcal/mol
Surface area14410 Å2
MethodPISA
2
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0709
Polymers101,8846
Non-polymers1863
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area16530 Å2
ΔGint-56 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.330, 111.330, 111.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUAA1 - 275 - 31
21METMETGLUGLUBB1 - 275 - 31
12VALVALGLYGLYAA70 - 7774 - 81
22VALVALGLYGLYBB70 - 7774 - 81
13ALAALAASNASNAA80 - 9284 - 96
23ALAALAASNASNBB80 - 9284 - 96
14THRTHRGLYGLYAA100 - 106104 - 110
24THRTHRGLYGLYBB100 - 106104 - 110
15ILEILEVALVALAA113 - 120117 - 124
25ILEILEVALVALBB113 - 120117 - 124

-
Components

#1: Protein Nucleoside diphosphate kinase / NDP kinase / NDPK / NDK


Mass: 16980.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU06_1530, HM-1:IMSS, NDK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SRM7, nucleoside-diphosphate kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PACT SCREEN CONDITION F8: 100MM BIS-TRIS PROPANE PH 6.5, 20% PEG 3350, 200 MM NA2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97651
20.97651
ReflectionResolution: 2.08→33.57 Å / Num. all: 28061 / Num. obs: 27311 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 33.82 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.88
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2051 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NSQ (Drosophila NDP kinase)

1nsq


Resolution: 2.08→33.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.51 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1385 5.1 %RANDOM
Rwork0.175 ---
all0.177 28061 --
obs0.177 27246 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.99 Å2
Refinement stepCycle: LAST / Resolution: 2.08→33.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 4 216 2536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222402
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.963245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65923.46998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1615449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6051516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211772
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_it0.7111.51482
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28722406
X-RAY DIFFRACTIONr_scbond_it2.2553920
X-RAY DIFFRACTIONr_scangle_it3.6864.5833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 504 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.110.5
medium thermal0.882
LS refinement shellResolution: 2.08→2.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 85 -
Rwork0.221 1873 -
obs-1959 95.47 %
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)
11.73890.4993-0.00861.5891-0.28021.32710.07710.09910.05770.15640.06270.1082-0.1968-0.2926-0.13980.07670.09460.01930.13660.01820.026328.5866-3.841769.9927
26.6351-0.24262.69522.9795-4.702312.37030.2332-0.08230.41970.14450.03430.2863-0.3647-0.8068-0.26750.18340.14990.09160.284-0.0260.137816.20172.417385.456
32.22121.17960.06632.01430.35792.52350.02050.09320.01120.11840.04580.2408-0.0702-0.3704-0.06630.0690.10180.03250.19670.02590.060223.6887-6.780773.2864
41.3354-0.3109-0.29011.49790.29973.5501-0.03470.08710.04730.1520.05320.2337-0.2192-0.6195-0.01850.04170.06540.02680.14970.02150.052122.78-8.211371.1259
51.73890.80870.2441.5028-0.17050.8864-0.01310.18360.1139-0.08570.11840.005-0.2398-0.2529-0.10540.17010.09250.00030.1550.03370.06835.41422.339659.9858
62.9174-1.4644-0.92333.49841.353111.60950.0704-0.0717-0.01140.08040.18940.0094-0.0353-0.3506-0.25980.17610.0141-0.09280.23790.07860.083229.15929.482241.2739
72.05571.21850.80713.0157-0.07051.7708-0.08740.27630.2301-0.05160.1528-0.0274-0.2905-0.1298-0.06540.17170.0810.00770.14790.06270.069837.42376.358455.923
81.2033-0.23470.69651.37070.13052.99590.01320.19970.2316-0.05640.0114-0.0564-0.5556-0.2579-0.02460.1750.06550.01950.10130.06340.069338.67678.14158.5088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 40
2X-RAY DIFFRACTION2A41 - 62
3X-RAY DIFFRACTION3A63 - 90
4X-RAY DIFFRACTION4A91 - 147
5X-RAY DIFFRACTION5B1 - 40
6X-RAY DIFFRACTION6B41 - 62
7X-RAY DIFFRACTION7B63 - 90
8X-RAY DIFFRACTION8B91 - 147

+
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