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- PDB-1nhk: CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KI... -

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Basic information

Entry
Database: PDB / ID: 1nhk
TitleCRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION
ComponentsNUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm
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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsStrelkov, S. / Williams, R.L.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: The 1.9 A crystal structure of a nucleoside diphosphate kinase complex with adenosine 3',5'-cyclic monophosphate: evidence for competitive inhibition.
Authors: Strelkov, S.V. / Perisic, O. / Webb, P.A. / Williams, R.L.
History
DepositionDec 9, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7094
Polymers32,0512
Non-polymers6582
Water3,945219
1
R: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules

R: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4188
Polymers64,1024
Non-polymers1,3174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)63.600, 63.600, 158.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0008, -0.9883, 0.1525), (-0.9869, -0.0237, -0.1593), (0.1611, -0.1506, -0.9754)
Vector: 66.8586, 67.6224, -0.457)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 L 2 - L 144 R 2 - R 144 0.230

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE KINASE / Nucleoside-diphosphate kinase


Mass: 16025.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: CMP / Plasmid: PUC119 DERIVED / Production host: Escherichia coli (E. coli) / References: UniProt: P15266, nucleoside-diphosphate kinase
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFOR EACH POLYPEPTIDE CHAIN THE SINGLE CAMP MOLECULE BOUND TO IT WAS MODELED WITH TWO ALTERNATIVE ...FOR EACH POLYPEPTIDE CHAIN THE SINGLE CAMP MOLECULE BOUND TO IT WAS MODELED WITH TWO ALTERNATIVE CONFORMERS, SYN AND ANTI. THE TWO ALTERNATIVES CORRESPONDING TO PROTEIN CHAIN R ARE DESIGNATED AS CMP 1 WITH ALTERNATE LOCATION INDICATORS A AND B, AND THE TWO ALTERNATIVES CORRESPONDING TO CHAIN L ARE DESIGNATED AS CMP 2 WITH ALTERNATE LOCATION INDICATORS A AND B. THE REFINEMENT WAS CARRIED OUT ON ALL CHAINS SIMULTANEOUSLY. THE DISORDER IN CAMP IS PRINCIPALLY MANIFEST IN THE POSITION OF THE BASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 mg/mlnucleoside diphosphate kinase1drop
28 mMcAMP1drop
31 mMEDTA1drop
410 mMTris-HCl1drop
513 %PEG30001drop
650 mMacetic acid1drop
7250 mMsodium acetate1drop
818 %PEG30001reservoir
950 mMacetic acid1reservoir
10250 mMsodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 26296 / % possible obs: 99.1 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 27 Å / Redundancy: 4.3 % / Num. measured all: 113713 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.9→6 Å / σ(F): 0
RfactorNum. reflection
Rfree0.206 -
Rwork0.174 -
obs0.174 25297
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 88 219 2554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 22.4

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