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- PDB-3ztp: Orthorhombic crystal form P21212 of the Aquifex aeolicus nucleosi... -

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Basic information

Entry
Database: PDB / ID: 3ztp
TitleOrthorhombic crystal form P21212 of the Aquifex aeolicus nucleoside diphosphate kinase
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / 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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsBoissier, F. / Georgescauld, F. / Moynie, L. / Dupuy, J.-W. / Sarger, C. / Podar, M. / Lascu, I. / Giraud, M.-F. / Dautant, A.
Citation
Journal: Proteins / Year: 2012
Title: An Intersubunit Disulfide Bridge Stabilizes the Tetrameric Nucleoside Diphosphate Kinase of Aquifex Aeolicus.
Authors: Boissier, F. / Georgescauld, F. / Moynie, L. / Dupuy, J.W. / Sarger, C. / Podar, M. / Lascu, I. / Giraud, M.F. / Dautant, A.
#1: Journal: Proteins / Year: 2007
Title: The Structure of the Escherichia Coli Nucleoside Diphosphate Kinase Reveals a New Quaternary Architecture for This Enzyme Family.
Authors: Moynie, L. / Giraud, M. / Georgescauld, F. / Lascu, I. / Dautant, A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and its Interaction with a Nucleotide Substrate at 2.0 A Resolution.
Authors: Williams, R.L. / Oren, D.A. / Munoz-Dorado, J. / Inouye, S. / Inouye, M. / Arnold, E.
History
DepositionJul 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: 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
C: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2115
Polymers31,9272
Non-polymers2843
Water6,413356
1
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)64,42210
Polymers63,8534
Non-polymers5686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6550 Å2
ΔGint-110.8 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.180, 95.120, 61.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2097-

HOH

21A-2187-

HOH

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE KINASE / NDK / NDP KINASE / NUCLEOSIDE-2-P KINASE


Mass: 15963.325 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67528, nucleoside-diphosphate kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.44 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growpH: 7.5 / Details: 2.0 M AMMONIUM FORMATE, 0.1 M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2009 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.37→23.31 Å / Num. obs: 65505 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 11.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 1.37→1.43 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZTO

3zto


Resolution: 1.37→23.313 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 13.7 / Stereochemistry target values: ML
Details: IN THE SSBOND CARDS: THE FIRST ATOM BELONGS TO THE ALTERNATE CONFORMER A (WITH OCCUPANCY Q1). THE SECOND ONE BELONGS TO THE ALTERNATE CONFORMER B (WITH OCCUPANCY Q2). ABS(Q1 - Q2)*100 IS THE ...Details: IN THE SSBOND CARDS: THE FIRST ATOM BELONGS TO THE ALTERNATE CONFORMER A (WITH OCCUPANCY Q1). THE SECOND ONE BELONGS TO THE ALTERNATE CONFORMER B (WITH OCCUPANCY Q2). ABS(Q1 - Q2)*100 IS THE PERCENTAGE OF CYS133 NOT INVOLVED IN THE DISULFIDE BRIDGE.
RfactorNum. reflection% reflection
Rfree0.1616 3212 5 %
Rwork0.1445 --
obs0.1454 64327 98.15 %
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.221 Å2 / ksol: 0.478 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.5528 Å20 Å20 Å2
2--0.1782 Å20 Å2
3----0.731 Å2
Refinement stepCycle: LAST / Resolution: 1.37→23.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 16 356 2602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012493
X-RAY DIFFRACTIONf_angle_d1.3253388
X-RAY DIFFRACTIONf_dihedral_angle_d13.15994
X-RAY DIFFRACTIONf_chiral_restr0.077363
X-RAY DIFFRACTIONf_plane_restr0.008453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.4190.27262800.24895301X-RAY DIFFRACTION86
1.419-1.47580.24413130.21835934X-RAY DIFFRACTION96
1.4758-1.54290.17753440.17036125X-RAY DIFFRACTION100
1.5429-1.62420.15933570.14086142X-RAY DIFFRACTION100
1.6242-1.7260.17192760.1396220X-RAY DIFFRACTION100
1.726-1.85920.14883430.13386160X-RAY DIFFRACTION100
1.8592-2.04620.13653020.12346227X-RAY DIFFRACTION100
2.0462-2.3420.14043150.12186246X-RAY DIFFRACTION100
2.342-2.94980.14143190.1296338X-RAY DIFFRACTION100
2.9498-23.31640.1693630.15236422X-RAY DIFFRACTION99
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)
10.37120.20540.09310.69540.02991.0248-0.00660.0261-0.0009-0.0080.00930.03170.0663-0.1539-0.00390.0184-0.0186-0.00210.05050.00020.014714.3299-4.9306-9.6471
25.12742.1597-0.42920.9609-0.08590.2115-0.08450.00210.2554-0.01080.01020.20770.0609-0.03590.03070.1743-0.15960.04260.3216-0.08480.1933.3762-14.46640.8018
30.2064-0.0629-0.11410.7728-0.09591.0356-0.0066-0.02120.00650.03790.00120.039-0.1206-0.16770.00180.07340.03010.00160.0845-0.0010.050716.68938.515121.6137
40.39670.16370.11540.06950.04770.039-0.0677-0.26180.1769-0.0270.0380.10760.03570.09620.04660.23890.212-0.08840.4528-0.07980.318.477819.659611.5567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 52:57 AND NOT ELEMENT H)
3X-RAY DIFFRACTION3(CHAIN C AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
4X-RAY DIFFRACTION4(CHAIN C AND RESSEQ 52:57 AND NOT ELEMENT H)

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