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- PDB-1xqi: Crystal Structure Analysis of an NDP kinase from Pyrobaculum aero... -

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Basic information

Entry
Database: PDB / ID: 1xqi
TitleCrystal Structure Analysis of an NDP kinase from Pyrobaculum aerophilum
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / alpha/beta sandwich / ferredoxin fold
Function / homology
Function and homology information


nucleoside-diphosphate kinase / nucleotide metabolic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / 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
TRIETHYLENE GLYCOL / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsPedelacq, J.D. / Waldo, G.S. / Cabantous, S. / Liong, E.C. / Berendzen, J. / Terwilliger, T.C.
CitationJournal: Protein Sci. / Year: 2005
Title: Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum
Authors: Pedelacq, J.D. / Waldo, G.S. / Cabantous, S. / Liong, E.C. / Terwilliger, T.C.
History
DepositionOct 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9069
Polymers66,0893
Non-polymers8176
Water2,846158
1
A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6046
Polymers44,0592
Non-polymers5454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint13 kcal/mol
Surface area17440 Å2
MethodPISA
2
B: Nucleoside diphosphate kinase
hetero molecules

B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6046
Polymers44,0592
Non-polymers5454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
3
B: Nucleoside diphosphate kinase
hetero molecules

B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,81218
Polymers132,1786
Non-polymers1,63412
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15860 Å2
ΔGint26 kcal/mol
Surface area45180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.022, 72.041, 104.993
Angle α, β, γ (deg.)90.00, 133.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleoside diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 22029.693 Da / Num. of mol.: 3 / Mutation: A10D, G33D, E40K, R71Q, S107N, I117N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: STRAIN IM2 DSM 7523 ATCC 51768 / Gene: ndk / Plasmid: modified pET 28 C-6HIS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZWY4, nucleoside-diphosphate kinase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9792, 0.9791, 0.9500
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2000 / Details: mirrors
RadiationMonochromator: Si 111 double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97911
30.951
ReflectionResolution: 2.4→25 Å / Num. all: 25584 / Num. obs: 22330 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.105
Reflection shellResolution: 2.4→2.55 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.26 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.594 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25964 1620 7.2 %RANDOM
Rwork0.18668 ---
obs0.19201 20785 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-0.82 Å2
2--0.62 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4242 0 54 158 4454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224365
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8862.0065897
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.96323.575179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30815744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9811538
X-RAY DIFFRACTIONr_chiral_restr0.1150.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023211
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.22020
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22949
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.2117
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9481.52821
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59624421
X-RAY DIFFRACTIONr_scbond_it2.54931733
X-RAY DIFFRACTIONr_scangle_it4.154.51476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 126 -
Rwork0.237 1568 -
obs--98.43 %

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