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- PDB-3mpd: Crystal structure of nucleoside diphosphate kinase from encephali... -

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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 / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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

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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
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

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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

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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: 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

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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

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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

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