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- PDB-3vpd: LysX from Thermus thermophilus complexed with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 3vpd
TitleLysX from Thermus thermophilus complexed with AMP-PNP
ComponentsRibosomal protein S6 modification protein
KeywordsLIGASE / ATP-dependenet amine/thiol ligase family / ATP-dependenet amine/thiol ligase
Function / homology
Function and homology information


[amino-group carrier protein]-L-2-aminoadipate ligase / lysine biosynthetic process / lysine biosynthetic process via aminoadipic acid / ligase activity / catalytic activity / protein modification process / ATP binding / metal ion binding
Similarity search - Function
Lysine biosynthesis enzyme LysX / LysX preATP-grasp domain / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...Lysine biosynthesis enzyme LysX / LysX preATP-grasp domain / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / butanoic acid / CITRIC ACID / Ribosomal protein S6 modification protein / Alpha-aminoadipate--LysW ligase LysX
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTomita, T. / Ouchi, T. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.
Authors: Ouchi, T. / Tomita, T. / Horie, A. / Yoshida, A. / Takahashi, K. / Nishida, H. / Lassak, K. / Taka, H. / Mineki, R. / Fujimura, T. / Kosono, S. / Nishiyama, C. / Masui, R. / Kuramitsu, S. / ...Authors: Ouchi, T. / Tomita, T. / Horie, A. / Yoshida, A. / Takahashi, K. / Nishida, H. / Lassak, K. / Taka, H. / Mineki, R. / Fujimura, T. / Kosono, S. / Nishiyama, C. / Masui, R. / Kuramitsu, S. / Albers, S.V. / Kuzuyama, T. / Nishiyama, M.
History
DepositionFeb 29, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: Ribosomal protein S6 modification protein
B: Ribosomal protein S6 modification protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0287
Polymers61,6472
Non-polymers1,3815
Water7,530418
1
A: Ribosomal protein S6 modification protein
B: Ribosomal protein S6 modification protein
hetero molecules

A: Ribosomal protein S6 modification protein
B: Ribosomal protein S6 modification protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,05514
Polymers123,2944
Non-polymers2,76110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area14600 Å2
ΔGint-51 kcal/mol
Surface area40610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.339, 130.339, 77.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ribosomal protein S6 modification protein / TtLysX / RimK


Mass: 30823.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: LysX, rimK / Plasmid: pET-TtLysX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3)
References: UniProt: O50144, UniProt: Q5SH23*PLUS, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: 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
#3: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5% PEG 400, 1.0M ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2010
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 55332 / Num. obs: 55332 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.95→1.98 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UC8

1uc8


Resolution: 1.95→49.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.39 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23777 2800 5.1 %RANDOM
Rwork0.19639 ---
obs0.19845 52342 99.72 %-
all-55332 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.891 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 87 418 4741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9996029
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54822.67191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16715734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3951546
X-RAY DIFFRACTIONr_chiral_restr0.1080.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213338
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8731.52736
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64424386
X-RAY DIFFRACTIONr_scbond_it2.47131697
X-RAY DIFFRACTIONr_scangle_it4.2484.51639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 199 -
Rwork0.248 3846 -
obs--99.41 %

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