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- PDB-7kpf: NME2 bound to myristoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 7kpf
TitleNME2 bound to myristoyl-CoA
ComponentsNucleoside diphosphate kinase B
KeywordsTRANSFERASE / NDPK / nucleoside diphosphate kinase / NME2 / myristoyl-CoA
Function / homology
Function and homology information


regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process ...regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / histidine kinase / ruffle / positive regulation of epithelial cell proliferation / cell periphery / integrin-mediated signaling pathway / GDP binding / lamellipodium / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / transcription coactivator activity / cell adhesion / Neutrophil degranulation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
TETRADECANOYL-COA / Nucleoside diphosphate kinase B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsPrice, I.R. / Lin, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM086703-07 United States
CitationJournal: To Be Published
Title: A Chemical Proteomic Approach reveals the regulation of NME1/2 and cancer metastasis by Long-Chain Fatty Acyl Coenzyme A
Authors: Zhang, S. / Nelson, O.D. / Price, I.R. / Zhu, C. / Fernandez, I.R. / Lu, X. / Weiss, R.S. / Lin, H.
History
DepositionNov 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase B
B: Nucleoside diphosphate kinase B
C: Nucleoside diphosphate kinase B
D: Nucleoside diphosphate kinase B
E: Nucleoside diphosphate kinase B
F: Nucleoside diphosphate kinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,14017
Polymers103,9446
Non-polymers3,19611
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Also supported by other crystal structures.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17390 Å2
ΔGint-140 kcal/mol
Surface area35020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.727, 107.515, 115.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoside diphosphate kinase B / NDP kinase B / C-myc purine-binding transcription factor PUF / Histidine protein kinase NDKB / nm23-H2


Mass: 17324.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME2, NM23B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P22392, nucleoside-diphosphate kinase, histidine kinase
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.78 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: The 2 mM NME2 protein (in 30 mM HEPES pH 8, 1 mM EDTA, 1 mM DTT) was mixed at a 1:1.1 ratio with 2 mM myristoyl-CoA in water and incubated on ice for 15 min. crystallized by vapor diffusion ...Details: The 2 mM NME2 protein (in 30 mM HEPES pH 8, 1 mM EDTA, 1 mM DTT) was mixed at a 1:1.1 ratio with 2 mM myristoyl-CoA in water and incubated on ice for 15 min. crystallized by vapor diffusion at 20 degrees C with a well solution of 10% PEG-4000, 100 mM MgCl2, 100 mM HEPES pH 7.5 and a protein-to-well drop ratio of 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.18→115.08 Å / Num. obs: 52327 / % possible obs: 94.7 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.041 / Rrim(I) all: 0.111 / Net I/σ(I): 13.2 / Num. measured all: 375490 / Scaling rejects: 104
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2% possible allRmerge(I) obsRpim(I) allRrim(I) allNet I/σ(I) obs
2.18-2.256.51382621390.59747.6
9.26-115.086.249818050.99896.80.030.0130.03346.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13-2998-0000refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BBF

3bbf


Resolution: 2.23→78.56 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2291 --
Rwork0.1901 --
obs-49376 96.15 %
Displacement parametersBiso max: 165.81 Å2 / Biso mean: 59.0708 Å2 / Biso min: 21.09 Å2
Refinement stepCycle: LAST / Resolution: 2.23→78.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6965 0 114 214 7293

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