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- PDB-1ank: THE CLOSED CONFORMATION OF A HIGHLY FLEXIBLE PROTEIN: THE STRUCTU... -

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Basic information

Entry
Database: PDB / ID: 1ank
TitleTHE CLOSED CONFORMATION OF A HIGHLY FLEXIBLE PROTEIN: THE STRUCTURE OF E. COLI ADENYLATE KINASE WITH BOUND AMP AND AMPPNP
ComponentsADENYLATE KINASE
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding ...purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Adenylate kinase / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBerry, M.B. / Meador, B. / Bilderback, T. / Liang, P. / Glaser, M. / Phillips Jr., G.N.
Citation
Journal: Proteins / Year: 1994
Title: The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP.
Authors: Berry, M.B. / Meador, B. / Bilderback, T. / Liang, P. / Glaser, M. / Phillips Jr., G.N.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Analysis of Escherichia Coli Adenylate Kinase
Authors: Althoff, S. / Zambrowicz, B. / Liang, P. / Glaser, M. / Phillips Jr., G.N.
History
DepositionFeb 28, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)48,9476
Polymers47,2402
Non-polymers1,7074
Water9,602533
1
A: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4733
Polymers23,6201
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4733
Polymers23,6201
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.700, 73.500, 79.600
Angle α, β, γ (deg.)90.00, 131.97, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 87 / 2: CIS PROLINE - PRO B 87
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4315, -0.0198, 0.9019), (0.0251, -0.9991, -0.0339), (0.9018, 0.0372, -0.4306)
Vector: 12.89, 10.356, 53.341)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein ADENYLATE KINASE


Mass: 23620.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P05082, UniProt: P69441*PLUS, adenylate kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.3 Mammonium sulfate1reservoir
2100 mMimidazole1reservoir
310 mMAMP1reservoir
410 mMAMPPNP1reservoir
52 mM1reservoirMgCl2
625 mg/mlprotein1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Num. obs: 30315 / % possible obs: 85.3 % / Num. measured all: 73378

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å
RfactorNum. reflection
Rfree0.316 -
Rwork0.201 -
obs0.201 30135
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 124 533 4725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.316 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.35

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