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

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Basic information

Entry
Database: PDB / ID: 4xym
TitleCa. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with coenzyme A, Ca-AMPCP and HgCl+
Components
  • alpha subunit of Acyl-CoA synthetase (NDP forming)
  • beta subunit of Acyl-CoA synthetase (NDP forming)
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 ADENOSYL ESTER / COENZYME A / : / Acyl-CoA synthetase (NDP forming) / ATP-grasp domain-containing protein
Similarity search - Component
Biological speciesKorarchaeum cryptofilum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 2, 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha subunit of Acyl-CoA synthetase (NDP forming)
B: beta subunit of Acyl-CoA synthetase (NDP forming)
C: alpha subunit of Acyl-CoA synthetase (NDP forming)
D: beta subunit of Acyl-CoA synthetase (NDP forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,36925
Polymers150,0634
Non-polymers4,30621
Water7,855436
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14720 Å2
ΔGint-401 kcal/mol
Surface area50460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.560, 114.416, 127.040
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 alpha subunit of Acyl-CoA synthetase (NDP forming)


Mass: 49354.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea)
Gene: Kcr_0198 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L3C9
#2: Protein beta subunit of Acyl-CoA synthetase (NDP forming)


Mass: 25676.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea)
Gene: Kcr_0115 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L7P8

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Non-polymers , 7 types, 457 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical ChemComp-A12 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE


Mass: 425.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.41 Å3/Da / Density % sol: 48.98 % / Description: rod-like appearance
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl (pH 8.3), 14% (w/v) PEG6000, 30 mM CaCl2, 2 mM HgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 1.9→127.04 Å / Num. all: 112092 / Num. obs: 112092 / % possible obs: 97.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 4.278 / Mean I/σ(I) obs: 0.3 / % possible all: 58.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSMarch 15, 2012data reduction
Aimless0.3.11data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→85.018 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 5591 5.03 %RANDOM
Rwork0.1953 ---
obs0.1974 111171 97.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→85.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10471 0 167 436 11074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710821
X-RAY DIFFRACTIONf_angle_d1.05614698
X-RAY DIFFRACTIONf_dihedral_angle_d12.5284039
X-RAY DIFFRACTIONf_chiral_restr0.0411688
X-RAY DIFFRACTIONf_plane_restr0.0051943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.92170.4918620.46161337X-RAY DIFFRACTION37
1.9217-1.94440.41661560.41263154X-RAY DIFFRACTION87
1.9444-1.96810.41621780.38393360X-RAY DIFFRACTION95
1.9681-1.9930.34741790.34753561X-RAY DIFFRACTION99
1.993-2.01920.32421600.33613609X-RAY DIFFRACTION100
2.0192-2.04690.34481880.32953578X-RAY DIFFRACTION100
2.0469-2.07610.39752120.35713496X-RAY DIFFRACTION98
2.0761-2.10710.28721910.29623600X-RAY DIFFRACTION100
2.1071-2.140.28341730.26953579X-RAY DIFFRACTION100
2.14-2.17510.31981930.2653595X-RAY DIFFRACTION100
2.1751-2.21260.25781940.26933604X-RAY DIFFRACTION100
2.2126-2.25290.38581920.32773536X-RAY DIFFRACTION98
2.2529-2.29620.28982010.25563581X-RAY DIFFRACTION99
2.2962-2.34310.28761930.22163591X-RAY DIFFRACTION100
2.3431-2.3940.24751920.20963585X-RAY DIFFRACTION100
2.394-2.44970.25672000.21133620X-RAY DIFFRACTION100
2.4497-2.5110.28811870.20233598X-RAY DIFFRACTION100
2.511-2.57890.24231890.19673622X-RAY DIFFRACTION100
2.5789-2.65480.25352180.20093595X-RAY DIFFRACTION100
2.6548-2.74050.25271760.19813629X-RAY DIFFRACTION100
2.7405-2.83840.25371680.18413638X-RAY DIFFRACTION100
2.8384-2.95210.25512190.19233621X-RAY DIFFRACTION100
2.9521-3.08640.2492100.19483607X-RAY DIFFRACTION100
3.0864-3.24920.26022040.19433623X-RAY DIFFRACTION100
3.2492-3.45270.23221780.18473670X-RAY DIFFRACTION100
3.4527-3.71930.22611920.16763636X-RAY DIFFRACTION100
3.7193-4.09360.18631960.15893665X-RAY DIFFRACTION100
4.0936-4.68590.15812000.13233685X-RAY DIFFRACTION100
4.6859-5.90360.17721900.14573728X-RAY DIFFRACTION100
5.9036-85.10330.17222000.14393877X-RAY DIFFRACTION99

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