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- PDB-2yep: STRUCTURE OF AN N-TERMINAL NUCLEOPHILE (NTN) HYDROLASE, OAT2, IN ... -

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Basic information

Entry
Database: PDB / ID: 2yep
TitleSTRUCTURE OF AN N-TERMINAL NUCLEOPHILE (NTN) HYDROLASE, OAT2, IN COMPLEX WITH GLUTAMATE
Components
  • (GLUTAMATE N-ACETYLTRANSFERASE 2 BETA ...) x 2
  • GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
KeywordsTRANSFERASE / ACYL ENZYME / NTN HYDROLASE / ACYLTRANSFERASE / ORNITHINE ACETYL TRANSFERASE / HYDROLASE
Function / homology
Function and homology information


glutamate N-acetyltransferase / glutamate N-acetyltransferase activity / ornithine biosynthetic process / methione N-acyltransferase activity / amino-acid N-acetyltransferase / clavulanic acid biosynthetic process / acetyl-CoA:L-glutamate N-acetyltransferase activity / arginine biosynthetic process / cytoplasm
Similarity search - Function
arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) ...arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GLUTAMIC ACID / Glutamate N-acetyltransferase 2 / Arginine biosynthesis bifunctional protein ArgJ 3
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChowdhury, R. / Iqbal, A. / Clifton, I.J. / Schofield, C.J.
CitationJournal: Org.Biomol.Chem. / Year: 2011
Title: Structural and Biochemical Analyses Reveal How Ornithine Acetyl Transferase Binds Acidic and Basic Amino Acid Substrates.
Authors: Iqbal, A. / Clifton, I.J. / Chowdhury, R. / Ivison, D. / Domene, C. / Schofield, C.J.
History
DepositionMar 29, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionSep 7, 2011ID: 2W4N
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source
Revision 2.0May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Polymer sequence
Category: entity_poly / exptl_crystal_grow ...entity_poly / exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.temp ..._entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_close_contact / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
B: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
C: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
D: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
E: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
F: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
G: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
H: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,22512
Polymers166,8138
Non-polymers4124
Water7,548419
1
A: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
B: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8613
Polymers41,7142
Non-polymers1471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-33.6 kcal/mol
Surface area15900 Å2
MethodPISA
2
C: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
D: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8613
Polymers41,7142
Non-polymers1471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-43.3 kcal/mol
Surface area19260 Å2
MethodPISA
3
E: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
F: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7313
Polymers41,6722
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-33.3 kcal/mol
Surface area15050 Å2
MethodPISA
4
G: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
H: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7733
Polymers41,7142
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-34 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.220, 73.424, 172.327
Angle α, β, γ (deg.)90.00, 93.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999829, -0.015048, -0.010744), (0.016346, 0.990947, 0.133252), (0.008641, -0.133405, 0.991024)-4.214, -25.932, -5.363
2given(0.790481, -0.031223, -0.61169), (-0.043143, -0.999057, -0.004757), (-0.610965, 0.030151, -0.791083)-19.115, 31.996, -68.116
3given(0.77566, -0.026282, -0.630604), (-0.094025, -0.992795, -0.074276), (-0.624108, 0.116905, -0.772543)-23.25, -3.657, -75.583
4given(0.99995, 0.00997, 0.000749), (-0.009984, 0.991762, 0.127707), (0.00053, -0.127708, 0.991812)-4.398, -26.011, -5.468
5given(0.806677, -0.006572, -0.590956), (-0.029791, -0.999119, -0.029553), (-0.590242, 0.041445, -0.806162)-19.985, 31.497, -68.94
6given(0.800696, -0.000496, -0.59907), (-0.076296, -0.991941, -0.101152), (-0.594192, 0.126699, -0.794282)-22.903, -4.505, -76.547

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Components

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Protein , 1 types, 4 molecules ACEG

#1: Protein
GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN / ORNITHINE ACETYLTRANSFERASE 2 ALPHA CHAIN / ORNITHINE TRANSACETYLASE 2 ALPHA CHAIN / OATASE 2 ALPHA CHAIN


Mass: 18837.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase

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GLUTAMATE N-ACETYLTRANSFERASE 2 BETA ... , 2 types, 4 molecules BDHF

#2: Protein GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE TRANSACETYLASE 2 BETA CHAIN / OATASE 2 BETA CHAIN


Mass: 22876.357 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase
#3: Protein GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE TRANSACETYLASE 2 BETA CHAIN / OATASE 2 BETA CHAIN


Mass: 22834.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase

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Non-polymers , 3 types, 423 molecules

#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Description: RMERGE AND REDUNDANCY VALUES NOT KNOWN, ESTIMATES GIVEN
Crystal growTemperature: 290 K / pH: 7.5
Details: 1.4M AMMONIUM SULPHATE, 100MM N-ACETYL -L-GLUTAMATE, 200MM NACL, 100MM TRIS HCL PH 7.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: OXFORD DIFFRACTION / Detector: CCD / Date: Nov 10, 2006 / Details: MULTI-LAYER OPTIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→61.12 Å / Num. obs: 60743 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.1
Reflection shell% possible all: 95.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VZ6, CHAIN A

1vz6


Resolution: 2.7→61.12 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3620114.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2209 5.4 %RANDOM
Rwork0.218 ---
obs0.218 40637 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.54 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.43 Å2
2--1.1 Å20 Å2
3----0.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.07 Å
Refinement stepCycle: LAST / Resolution: 2.7→61.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11206 0 26 419 11651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.236 156 5.1 %
Rwork0.223 2916 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TH5.PARTH5.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ACT.PARACT.TOP

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