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- PDB-1vya: Identification and characterization of the first plant G-quadrupl... -

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Basic information

Entry
Database: PDB / ID: 1vya
TitleIdentification and characterization of the first plant G-quadruplex binding protein encoded by the Zea mays L. nucleoside diphosphate1 gene, ZmNDPK1
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / G4-binding protein / NDPK / DNA metabolism / G-quadruplex
Function / homology
Function and homology information


nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / protein hexamerization / GTP biosynthetic process / nucleoside diphosphate kinase activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / 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 / Alpha-Beta Plaits ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKopylov, M. / Stroupe, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1149763 United States
CitationJournal: Biochemistry / Year: 2015
Title: The Maize (Zea mays L.) Nucleoside Diphosphate Kinase1 (ZmNDPK1) Gene Encodes a Human NM23-H2 Homologue That Binds and Stabilizes G-Quadruplex DNA.
Authors: Kopylov, M. / Bass, H.W. / Stroupe, M.E.
History
DepositionAug 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)198,92412
Polymers198,92412
Non-polymers00
Water29,9591663
1
A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)99,4626
Polymers99,4626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16520 Å2
ΔGint-56 kcal/mol
Surface area34110 Å2
MethodPISA
2
B: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)99,4626
Polymers99,4626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16620 Å2
ΔGint-57 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.962, 179.198, 88.469
Angle α, β, γ (deg.)90.00, 99.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoside diphosphate kinase


Mass: 16576.971 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Strain: W23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: B4FK49*PLUS, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1663 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate (pH 6.5), 12% PEG 8000, and 200 mM CaCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 123697 / % possible obs: 96.31 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.8
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.75 / % possible all: 92.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8W

1u8w


Resolution: 2.05→39.859 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 19.5 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 1700 1.37 %Random selection
Rwork0.1603 ---
obs0.1609 123697 96.31 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.059 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.9006 Å2-0 Å2-2.9781 Å2
2---0.9921 Å2-0 Å2
3----1.9085 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14040 0 0 1663 15703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715027
X-RAY DIFFRACTIONf_angle_d1.01320451
X-RAY DIFFRACTIONf_dihedral_angle_d14.3845699
X-RAY DIFFRACTIONf_chiral_restr0.0722226
X-RAY DIFFRACTIONf_plane_restr0.0042615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11030.25671000.20079573X-RAY DIFFRACTION91
2.1103-2.17840.26911000.18129766X-RAY DIFFRACTION93
2.1784-2.25630.24042000.17739806X-RAY DIFFRACTION94
2.2563-2.34660.21741000.17569964X-RAY DIFFRACTION94
2.3466-2.45340.23782000.175410012X-RAY DIFFRACTION95
2.4534-2.58270.211000.172110203X-RAY DIFFRACTION96
2.5827-2.74450.21482000.16910142X-RAY DIFFRACTION97
2.7445-2.95630.21521000.175310377X-RAY DIFFRACTION98
2.9563-3.25370.18961110.165310465X-RAY DIFFRACTION99
3.2537-3.72430.20451890.155210509X-RAY DIFFRACTION100
3.7243-4.6910.15251000.129610587X-RAY DIFFRACTION100
4.691-39.86640.16892000.146710593X-RAY DIFFRACTION100

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