[English] 日本語
Yorodumi
- PDB-9oak: Crystal structure of nucleoside-diphosphate kinase from Cryptospo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9oak
TitleCrystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with cytidine-5'-diphosphate and cytidine-5'-triphosphate
Componentsnucleoside-diphosphate kinase
KeywordsTRANSFERASE / SSGCID / 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
Similarity search - Function
Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / nucleoside-diphosphate kinase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with cytidine-5'-diphosphate and cytidine-5'-triphosphate
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: nucleoside-diphosphate kinase
B: nucleoside-diphosphate kinase
C: nucleoside-diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0127
Polymers53,0773
Non-polymers9354
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-33 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.734, 69.734, 316.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

21C-374-

HOH

-
Components

#1: Protein nucleoside-diphosphate kinase


Mass: 17692.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd4_1940 / Plasmid: CrpaA.01302.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5CR64, nucleoside-diphosphate kinase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Berkeley F12: 25% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystals soaked for 4 hours in 10mM ligand, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, ...Details: Berkeley F12: 25% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystals soaked for 4 hours in 10mM ligand, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Subunit A contains partially occupied CTP and HIP from reaction. Subunit C contains partially occupied CDP and HIP. plate Liu-S-177 D2, Puck: PSL-0503, Cryo: direct from soaking solution

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 5, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.61→47.99 Å / Num. obs: 60534 / % possible obs: 100 % / Redundancy: 16.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.024 / Rrim(I) all: 0.102 / Χ2: 0.94 / Net I/σ(I): 19.8 / Num. measured all: 1023118
Reflection shellResolution: 1.61→1.65 Å / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.869 / Num. measured all: 32252 / Num. unique obs: 4362 / CC1/2: 0.765 / Rpim(I) all: 0.335 / Rrim(I) all: 0.934 / Χ2: 0.68 / Net I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
PHENIX(dev_5669: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→47.99 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1715 3014 4.99 %
Rwork0.1449 --
obs0.1462 60366 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 56 429 4004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093765
X-RAY DIFFRACTIONf_angle_d1.0475120
X-RAY DIFFRACTIONf_dihedral_angle_d16.4091517
X-RAY DIFFRACTIONf_chiral_restr0.058563
X-RAY DIFFRACTIONf_plane_restr0.011655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.640.29061520.27442526X-RAY DIFFRACTION100
1.64-1.660.24331270.22382575X-RAY DIFFRACTION100
1.66-1.690.2269970.1912548X-RAY DIFFRACTION100
1.69-1.720.22161340.17492548X-RAY DIFFRACTION100
1.72-1.750.21751280.16432567X-RAY DIFFRACTION100
1.75-1.790.19321340.15252566X-RAY DIFFRACTION100
1.79-1.830.19161310.14722569X-RAY DIFFRACTION100
1.83-1.870.16781320.15022527X-RAY DIFFRACTION100
1.87-1.920.17441560.15182547X-RAY DIFFRACTION100
1.92-1.970.17921330.1532572X-RAY DIFFRACTION100
1.97-2.030.17241570.132553X-RAY DIFFRACTION100
2.03-2.090.16061280.12712591X-RAY DIFFRACTION100
2.09-2.170.14381390.12422592X-RAY DIFFRACTION100
2.17-2.260.16741400.1282583X-RAY DIFFRACTION100
2.26-2.360.17851440.12952576X-RAY DIFFRACTION100
2.36-2.480.15571290.13722625X-RAY DIFFRACTION100
2.48-2.640.18471450.1472613X-RAY DIFFRACTION100
2.64-2.840.1591130.14582658X-RAY DIFFRACTION100
2.84-3.130.15831220.1442674X-RAY DIFFRACTION100
3.13-3.580.16581490.13782671X-RAY DIFFRACTION100
3.58-4.510.1361600.12352729X-RAY DIFFRACTION100
4.51-47.990.19261640.16332942X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.0974 Å / Origin y: 28.7826 Å / Origin z: 14.1556 Å
111213212223313233
T0.1216 Å20.0247 Å20.0001 Å2-0.1407 Å20.0079 Å2--0.1084 Å2
L0.4051 °2-0.0501 °20.0078 °2-0.2672 °20.0548 °2--0.3715 °2
S0.0075 Å °0.0539 Å °0.0099 Å °-0.0521 Å °-0.014 Å °0.0085 Å °0.0274 Å °0.0281 Å °0.0069 Å °
Refinement TLS groupSelection details: all

+
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