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- PDB-4iz9: Crystal structure of an acetate kinase from Mycobacterium avium b... -

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Basic information

Entry
Database: PDB / ID: 4iz9
TitleCrystal structure of an acetate kinase from Mycobacterium avium bound to an unknown acid-ApCpp conjugate and manganese
ComponentsAcetate kinase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / AckA / propionate kinase / acid-kinase / ATP-dependent / non-hydrolyzable ATP analog / anomalous manganese signal / unknown conjugate
Function / homology
Function and homology information


acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / SUCCINIC ACID / Acetate kinase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5788
Polymers41,6511
Non-polymers9277
Water5,405300
1
A: Acetate kinase
hetero molecules

A: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,15516
Polymers83,3022
Non-polymers1,85314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10280 Å2
ΔGint-19 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.770, 95.770, 141.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-708-

HOH

31A-754-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetate kinase / Acetokinase


Mass: 41651.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: ackA / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QLU8, acetate kinase

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Non-polymers , 5 types, 307 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MyavA.00640.a.A1 PS00663 at 20 mg/mL with 2 mM ApCpp and 2 mM MnCl2 against PACT screen condition A4, 0.1 M SPG buffer pH 7.0, 25% PEG 3350 and 15% ethylene glycol as cryo-protectant, ...Details: MyavA.00640.a.A1 PS00663 at 20 mg/mL with 2 mM ApCpp and 2 mM MnCl2 against PACT screen condition A4, 0.1 M SPG buffer pH 7.0, 25% PEG 3350 and 15% ethylene glycol as cryo-protectant, crystal tracking ID 236958a4, unique puck ID lqa0-2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 8, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 44007 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 34.164 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 17.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.98-2.260.5246.34348222489100
2.26-2.320.4327.5833602239499.8
2.32-2.390.3738.3633324234599.9
2.39-2.460.3448.8732546228199.9
2.46-2.540.3099.4531460220299.9
2.54-2.630.25510.88304182127100
2.63-2.730.22611.8429591207499.9
2.73-2.840.19512.5828574199399.9
2.84-2.970.18612.5827649192099.9
2.97-3.110.15414.9264421841100
3.11-3.280.12818.95251241756100
3.28-3.480.10424.44234931664100
3.48-3.720.08530.27215981578100
3.72-4.020.07632.29196881464100
4.02-4.40.06635.5218029135099.9
4.4-4.920.05938.8916263123499.3
4.92-5.680.05937.814810111299.9
5.68-6.960.06334.0512908954100
6.96-9.840.04341.979751757100
9.840.03945.74464839385.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3p4i

3p4i


Resolution: 1.98→45.39 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1917 / WRfactor Rwork: 0.1621 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8843 / SU B: 4.95 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1136 / SU Rfree: 0.1117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 2348 5.1 %RANDOM
Rwork0.1725 ---
obs0.1741 44007 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.76 Å2 / Biso mean: 39.2756 Å2 / Biso min: 14.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0 Å2
2---0.37 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.98→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 55 300 3185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193051
X-RAY DIFFRACTIONr_bond_other_d0.0010.022907
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9994165
X-RAY DIFFRACTIONr_angle_other_deg0.80636653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9815400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66422.061131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72815464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.831535
X-RAY DIFFRACTIONr_chiral_restr0.0830.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
X-RAY DIFFRACTIONr_mcbond_it1.6242.8951547
X-RAY DIFFRACTIONr_mcbond_other1.6242.8931546
X-RAY DIFFRACTIONr_mcangle_it2.4644.3191937
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 184 -
Rwork0.228 3182 -
all-3366 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 14.9578 Å / Origin y: 39.5918 Å / Origin z: 5.8384 Å
111213212223313233
T0.0274 Å2-0.0037 Å20.0137 Å2-0.0083 Å2-0.0049 Å2--0.0501 Å2
L0.3983 °20.0985 °20.0322 °2-0.5074 °20.2544 °2--0.1289 °2
S0.009 Å °0.0134 Å °0.1175 Å °0.0516 Å °-0.052 Å °0.108 Å °0.0285 Å °-0.0232 Å °0.043 Å °

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