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- PDB-3wwm: Crystal structure of LysZ from Thermus thermophilus with ADP -

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Basic information

Entry
Database: PDB / ID: 3wwm
TitleCrystal structure of LysZ from Thermus thermophilus with ADP
ComponentsPutative acetylglutamate kinase-like protein
KeywordsTRANSFERASE / Amino acid kinase
Function / homology
Function and homology information


[amino-group carrier protein]-L-2-aminoadipate 6-kinase / N2-acetyl-L-aminoadipate kinase activity / lysine biosynthetic process via aminoadipic acid / ATP binding / cytoplasm
Similarity search - Function
[LysW]-aminoadipate/[LysW]-glutamate kinase / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / [LysW]-aminoadipate kinase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYoshida, A. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.
Authors: Yoshida, A. / Tomita, T. / Fujimura, T. / Nishiyama, C. / Kuzuyama, T. / Nishiyama, M.
History
DepositionJun 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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 / 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

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Assembly

Deposited unit
A: Putative acetylglutamate kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5622
Polymers29,1351
Non-polymers4271
Water48627
1
A: Putative acetylglutamate kinase-like protein
hetero molecules

A: Putative acetylglutamate kinase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1244
Polymers58,2692
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4330 Å2
ΔGint-32 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.490, 80.490, 152.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative acetylglutamate kinase-like protein


Mass: 29134.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1541 / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O50147
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4.23 Å3/Da / Density % sol: 70.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.1M tri-sodium citrate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2010
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 13007 / Num. obs: 13002 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Rsym value: 0.049 / Net I/σ(I): 59.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 8.7 / Num. unique all: 2355 / Rsym value: 0.394 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U6U

3u6u


Resolution: 2.8→42.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.212 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22546 628 4.9 %RANDOM
Rwork0.18657 ---
obs0.18843 12318 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å20 Å2
2---0.56 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 27 27 2102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192107
X-RAY DIFFRACTIONr_bond_other_d0.0010.022108
X-RAY DIFFRACTIONr_angle_refined_deg1.1912.0082857
X-RAY DIFFRACTIONr_angle_other_deg0.69334831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6745268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48623.37286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38715366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7681519
X-RAY DIFFRACTIONr_chiral_restr0.0570.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212359
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
X-RAY DIFFRACTIONr_mcbond_it1.4724.791075
X-RAY DIFFRACTIONr_mcbond_other1.4724.791074
X-RAY DIFFRACTIONr_mcangle_it2.4687.1851342
X-RAY DIFFRACTIONr_mcangle_other2.4677.1841343
X-RAY DIFFRACTIONr_scbond_it2.0385.2381031
X-RAY DIFFRACTIONr_scbond_other2.0375.2461032
X-RAY DIFFRACTIONr_scangle_other3.4517.7481516
X-RAY DIFFRACTIONr_long_range_B_refined5.638.8022257
X-RAY DIFFRACTIONr_long_range_B_other5.59838.822256
LS refinement shellResolution: 2.799→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 59 -
Rwork0.235 880 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.4882 Å / Origin y: -1.4117 Å / Origin z: 24.546 Å
111213212223313233
T0.1706 Å20.0436 Å20.0383 Å2-0.0683 Å20.0278 Å2--0.0169 Å2
L1.7115 °20.4555 °2-1.542 °2-2.9893 °2-0.7358 °2--2.7302 °2
S0.0371 Å °0.2611 Å °0.0651 Å °-0.3435 Å °0.0661 Å °-0.0723 Å °-0.3466 Å °-0.2931 Å °-0.1033 Å °

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