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- PDB-1zak: ADENYLATE KINASE FROM MAIZE IN COMPLEX WITH THE INHIBITOR P1,P5-B... -

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Basic information

Entry
Database: PDB / ID: 1zak
TitleADENYLATE KINASE FROM MAIZE IN COMPLEX WITH THE INHIBITOR P1,P5-BIS(ADENOSINE-5'-)PENTAPHOSPHATE (AP5A)
ComponentsADENYLATE KINASE
KeywordsTRANSFERASE / ATP:AMP-PHOSPHOTRANSFERASE
Function / homology
Function and homology information


: / cytidylate kinase activity / nucleoside triphosphate biosynthetic process / adenylate kinase / adenylate kinase activity / nucleoside diphosphate kinase activity / chloroplast / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWild, K. / Schulz, G.E.
Citation
Journal: Eur.J.Biochem. / Year: 1997
Title: Structure, catalysis and supramolecular assembly of adenylate kinase from maize.
Authors: Wild, K. / Grafmuller, R. / Wagner, E. / Schulz, G.E.
#1: Journal: Eur.J.Biochem. / Year: 1994
Title: Primary Structure of Maize Chloroplast Adenylate Kinase
Authors: Schiltz, E. / Burger, S. / Grafmuller, R. / Deppert, W.R. / Haehnel, W. / Wagner, E.
History
DepositionMay 31, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...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.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
A: ADENYLATE KINASE
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6284
Polymers49,7952
Non-polymers1,8332
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.300, 83.300, 69.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7065, 0.7077, 0.0046), (0.7077, 0.7065, -0.0029), (0.0012, -0.0053, -1)
Vector: 52.145, -21.328, 111.845)

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Components

#1: Protein ADENYLATE KINASE /


Mass: 24897.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / Cellular location: CYTOPLASM / Organelle: CHLOROPLAST / References: UniProt: P43188, adenylate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
Nonpolymer detailsTHE WATER MOLECULE MODELED INTO THE AMP-BINDING SITE TOGETHER WITH CMP HAS THE COORDINATES X Y Z 17. ...THE WATER MOLECULE MODELED INTO THE AMP-BINDING SITE TOGETHER WITH CMP HAS THE COORDINATES X Y Z 17.800 12.672 46.697 THIS IS FOR CHAIN A ONLY.

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlenzyme1drop
22 mMAp5A1drop
310 mMHEPES1drop
41 M1dropLi2SO4
510 %PEG80001drop
61 M1reservoirLi2SO4
710 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Apr 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.16→100 Å / Num. obs: 6998 / % possible obs: 75.4 % / Redundancy: 3 % / Rsym value: 0.074
Reflection shellResolution: 3.16→3.33 Å / Rsym value: 0.172 / % possible all: 53.3
Reflection
*PLUS
Rmerge(I) obs: 0.074

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
MERGEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKE

1ake


Resolution: 3.5→25 Å / Details: ONLY THE OVERALL B-FACTOR WAS REFINED.
RfactorNum. reflection% reflection
Rwork0.218 --
obs0.218 5578 81.8 %
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 3.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 57 0 1791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.76
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
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 3.5→3.66 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.243 583 -
obs--69.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.76

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