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- PDB-3zto: Orthorhombic crystal form C222 of the Aquifex aeolicus nucleoside... -

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Basic information

Entry
Database: PDB / ID: 3zto
TitleOrthorhombic crystal form C222 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 / nucleoside diphosphate kinase activity / GTP biosynthetic process / 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 / 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 ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / 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 speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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. / Sarger, C. / Podar, M. / Lascu, I. / Giraud, M. / 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 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1553
Polymers15,9631
Non-polymers1922
Water3,315184
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules

A: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules

A: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules

A: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,62212
Polymers63,8534
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area6960 Å2
ΔGint-174 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.130, 101.060, 62.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

21A-2050-

HOH

31A-2061-

HOH

41A-2062-

HOH

51A-2118-

HOH

61A-2152-

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.: 1
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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 5.5 / Details: 25% PEG 3350, 0.2 M LISO4, 0.1 M BIS-TRIS PH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2008 / Details: KIRKPATRICK BAEZ
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.47→15.54 Å / Num. obs: 23200 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 13.08 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.4
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

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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 1NLK

1nlk


Resolution: 1.47→15.763 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 16.51 / 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
Rfree0.1806 1197 5.2 %
Rwork0.1506 --
obs0.1522 23194 98.71 %
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.145 Å2 / ksol: 0.501 e/Å3
Displacement parametersBiso mean: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.0035 Å20 Å20 Å2
2---0.1847 Å20 Å2
3----3.8188 Å2
Refinement stepCycle: LAST / Resolution: 1.47→15.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 10 184 1306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081195
X-RAY DIFFRACTIONf_angle_d1.2161616
X-RAY DIFFRACTIONf_dihedral_angle_d13.536464
X-RAY DIFFRACTIONf_chiral_restr0.072175
X-RAY DIFFRACTIONf_plane_restr0.007212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.52880.27191270.26422376X-RAY DIFFRACTION97
1.5288-1.59830.23691260.2112450X-RAY DIFFRACTION100
1.5983-1.68250.23441400.17612429X-RAY DIFFRACTION100
1.6825-1.78780.20681240.16652441X-RAY DIFFRACTION100
1.7878-1.92560.15751380.15322440X-RAY DIFFRACTION100
1.9256-2.1190.19891530.12532440X-RAY DIFFRACTION99
2.119-2.42460.14571210.12632478X-RAY DIFFRACTION99
2.4246-3.05120.17811340.12862464X-RAY DIFFRACTION98
3.0512-15.76380.16011340.15192479X-RAY DIFFRACTION95
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)
10.3961-0.28190.11940.49180.13470.99190.02840.0121-0.0293-0.06330.0012-0.04150.10230.0913-0.02940.0782-0.00020.00090.0806-0.00380.07976.9539-10.5399-15.5561
20.3722-0.31410.15410.39240.14210.6787-0.01210.008-0.0020.0640.1255-0.04580.18830.1218-0.0680.29520.0636-0.01980.17760.00140.194717.9152-19.9564-5.2304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND (RESSEQ 2:51 OR RESSEQ 58:142))
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 52:57)

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