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- PDB-3wwn: Crystal structure of LysZ from Thermus thermophilus complex with LysW -

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Basic information

Entry
Database: PDB / ID: 3wwn
TitleCrystal structure of LysZ from Thermus thermophilus complex with LysW
Components
  • OrfF
  • Putative acetylglutamate kinase-like protein
KeywordsMETAL BINDING PROTEIN/TRANSFERASE / Zinc finger / Amino acid kinase / METAL BINDING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


[amino-group carrier protein]-L-2-aminoadipate 6-kinase / N2-acetyl-L-aminoadipate kinase activity / acetylglutamate kinase activity / lysine biosynthetic process via aminoadipic acid / L-arginine biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rubrerythrin, domain 2 - #160 / [LysW]-aminoadipate/[LysW]-glutamate kinase / Lysine biosynthesis protein LysW / Alpha-aminoadipate carrier protein LysW-like, globular domain / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily ...Rubrerythrin, domain 2 - #160 / [LysW]-aminoadipate/[LysW]-glutamate kinase / Lysine biosynthesis protein LysW / Alpha-aminoadipate carrier protein LysW-like, globular domain / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / TFIIB zinc-binding / Rubrerythrin, domain 2 / Single Sheet / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
[LysW]-aminoadipate kinase / Alpha-aminoadipate carrier protein LysW
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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
B: OrfF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1114
Polymers34,9492
Non-polymers1612
Water4,594255
1
A: Putative acetylglutamate kinase-like protein
B: OrfF
hetero molecules

A: Putative acetylglutamate kinase-like protein
B: OrfF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2218
Polymers69,8984
Non-polymers3234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area7420 Å2
ΔGint-69 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.809, 69.809, 148.036
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-457-

HOH

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Components

#1: Protein Putative acetylglutamate kinase-like protein / AAA carrier protein LysW


Mass: 29134.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O50147
#2: Protein OrfF / Lysine biosynthetic protein LysW


Mass: 5814.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9ZND7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% (v/w) PEG 8000, 0.1M MES pH 6.0, 0.2M Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2009
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: 1.85→50 Å / Num. all: 32240 / Num. obs: 32177 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Rsym value: 0.067 / Net I/σ(I): 46.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1582 / Rsym value: 0.72 / % possible all: 100

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Processing

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

3wwl

3u6u


Resolution: 1.85→28.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.027 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21282 1626 5.1 %RANDOM
Rwork0.17695 ---
obs0.17876 30470 99.76 %-
all-32240 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.605 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 6 255 2661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192447
X-RAY DIFFRACTIONr_bond_other_d0.0010.022432
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.0023315
X-RAY DIFFRACTIONr_angle_other_deg0.78835592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14523.942104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45415426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9351522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
X-RAY DIFFRACTIONr_mcbond_it1.5242.6961267
X-RAY DIFFRACTIONr_mcbond_other1.5232.6941266
X-RAY DIFFRACTIONr_mcangle_it2.4154.0251579
X-RAY DIFFRACTIONr_mcangle_other2.4154.0281580
X-RAY DIFFRACTIONr_scbond_it2.2663.0991180
X-RAY DIFFRACTIONr_scbond_other2.2653.1011181
X-RAY DIFFRACTIONr_scangle_other3.6984.4971736
X-RAY DIFFRACTIONr_long_range_B_refined6.86923.3582858
X-RAY DIFFRACTIONr_long_range_B_other6.6722.6572754
LS refinement shellResolution: 1.849→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 120 -
Rwork0.208 2191 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2929-0.0002-0.150.59610.14170.4886-0.0346-0.031-0.01760.00080.0095-0.08660.09540.06810.0250.04120.01040.01870.0517-0.01040.0261-29.808817.1076-1.9669
20.8296-1.2123-0.15286.0591-0.91570.5073-0.02030.0027-0.04930.02490.0139-0.1216-0.01070.01260.00640.1036-0.00310.04180.002-0.00690.0407-39.8621-2.5491.3683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2B1 - 101

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