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- PDB-4xz3: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -

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Basic information

Entry
Database: PDB / ID: 4xz3
TitleCa. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 (Se-Met derivative) in complex with coenzyme A and Mg-AMPPCP, phosphohistidine segment pointing towards nucleotide binding site
Components
  • Acyl-CoA synthetase (NDP forming)
  • Uncharacterized protein
KeywordsLIGASE / Dinucleotide forming acetyl-CoA synthetase / complex / ACD
Function / homology
Function and homology information


acetate-CoA ligase (ADP-forming) activity / ligase activity / nucleotide binding / ATP binding / metal ion binding
Similarity search - Function
Ligase-CoA domain / Ligase-CoA domain / : / Succinyl-CoA synthetase-like, flavodoxin domain / ATP-grasp domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase domains / Succinyl-CoA synthetase-like / CoA binding domain ...Ligase-CoA domain / Ligase-CoA domain / : / Succinyl-CoA synthetase-like, flavodoxin domain / ATP-grasp domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase domains / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / COENZYME A / Acyl-CoA synthetase (NDP forming) / ATP-grasp domain-containing protein
Similarity search - Component
Biological speciesCandidatus Korarchaeum cryptofilum OPF8 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsWeisse, R.H.-J. / Scheidig, A.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer.
Authors: Weie, R.H. / Faust, A. / Schmidt, M. / Schonheit, P. / Scheidig, A.J.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA synthetase (NDP forming)
B: Uncharacterized protein
C: Acyl-CoA synthetase (NDP forming)
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,33415
Polymers151,6574
Non-polymers3,67711
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15220 Å2
ΔGint-113 kcal/mol
Surface area51250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.170, 111.880, 127.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Acyl-CoA synthetase (NDP forming)


Mass: 49917.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Korarchaeum cryptofilum OPF8 (archaea)
Gene: Kcr_0198 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L3C9
#2: Protein Uncharacterized protein


Mass: 25911.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Korarchaeum cryptofilum OPF8 (archaea)
Gene: Kcr_0115 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L7P8

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Non-polymers , 4 types, 67 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.37 % / Description: rod-like appearance
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: protein buffer contained 20 mM DTT, 100 mM Tris/HCl (pH 8.3), 18% (w/v) PEG6000, 30 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97985 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionResolution: 2.398→48.84 Å / Num. all: 56770 / Num. obs: 56770 / % possible obs: 99.9 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 9.9
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 12.5 % / Rmerge(I) obs: 3.182 / Mean I/σ(I) obs: 0.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSJanuary 10, 2014data reduction
Aimless0.3.11data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.398→48.84 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 2877 5.07 %RANDOM
Rwork0.1965 ---
obs0.1989 56719 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.398→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10281 0 207 56 10544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410687
X-RAY DIFFRACTIONf_angle_d0.76314538
X-RAY DIFFRACTIONf_dihedral_angle_d11.7983971
X-RAY DIFFRACTIONf_chiral_restr0.0291674
X-RAY DIFFRACTIONf_plane_restr0.0041909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3982-2.43750.35221400.32542419X-RAY DIFFRACTION96
2.4375-2.47950.40211270.32852526X-RAY DIFFRACTION100
2.4795-2.52460.35421380.32332538X-RAY DIFFRACTION100
2.5246-2.57320.36751320.30642560X-RAY DIFFRACTION100
2.5732-2.62570.35221440.29212519X-RAY DIFFRACTION100
2.6257-2.68280.31441500.29182502X-RAY DIFFRACTION100
2.6828-2.74520.36581180.27342567X-RAY DIFFRACTION100
2.7452-2.81380.30841250.26412565X-RAY DIFFRACTION100
2.8138-2.88990.32421380.24932538X-RAY DIFFRACTION100
2.8899-2.97490.28711500.23022534X-RAY DIFFRACTION100
2.9749-3.07090.26841490.24142540X-RAY DIFFRACTION100
3.0709-3.18060.27711330.23022564X-RAY DIFFRACTION100
3.1806-3.3080.29171370.2292547X-RAY DIFFRACTION100
3.308-3.45850.25371300.19732587X-RAY DIFFRACTION100
3.4585-3.64080.24131390.18552553X-RAY DIFFRACTION100
3.6408-3.86880.22641410.16662589X-RAY DIFFRACTION100
3.8688-4.16730.21391350.15842594X-RAY DIFFRACTION100
4.1673-4.58640.1851400.13982580X-RAY DIFFRACTION100
4.5864-5.24940.17681250.14762609X-RAY DIFFRACTION100
5.2494-6.61110.2451390.17732654X-RAY DIFFRACTION100
6.6111-48.85030.17441470.15422757X-RAY DIFFRACTION100

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