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- PDB-1vra: Crystal structure of Arginine biosynthesis bifunctional protein a... -

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Basic information

Entry
Database: PDB / ID: 1vra
TitleCrystal structure of Arginine biosynthesis bifunctional protein argJ (10175521) from Bacillus halodurans at 2.00 A resolution
Components(Arginine biosynthesis bifunctional protein ...) x 2
KeywordsTRANSFERASE / 10175521 / arginine biosynthesis bifunctional protein argJ / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


glutamate N-acetyltransferase / L-glutamate N-acetyltransferase activity, acting on acetyl-L-ornithine as donor / ornithine biosynthetic process / amino-acid N-acetyltransferase / L-glutamate N-acetyltransferase activity / L-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
Unknown ligand / Arginine biosynthesis bifunctional protein ArgJ
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Arginine biosynthesis bifunctional protein argJ (10175521) from Bacillus halodurans at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE CLONING ARTIFACT: THE DENSITY FOR RESIDUE 252 SUGGESTS THAT THIS RESIDUE WAS A THREONINE ...SEQUENCE CLONING ARTIFACT: THE DENSITY FOR RESIDUE 252 SUGGESTS THAT THIS RESIDUE WAS A THREONINE AND NOT AN ALANINE. SEQUENCING OF THE CONSTRUCT IS CONSISTENT WITH RESIDUE 252 BEING A THREONINE IN THE EXPRESSED PROTEIN.
Remark 400COMPOUND THERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 196 AND 197. SIMILAR PROTEOLYSIS HAS BEEN ...COMPOUND THERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 196 AND 197. SIMILAR PROTEOLYSIS HAS BEEN SHOWN TO BE THE RESULT OF AUTO-PROTEOLYTIC SELF-ACTIVATION OF THE ENZYME IN HOMOLOGS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginine biosynthesis bifunctional protein argJ
B: Arginine biosynthesis bifunctional protein argJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,73221
Polymers45,5472
Non-polymers1,18519
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-25 kcal/mol
Surface area15160 Å2
MethodPISA
2
A: Arginine biosynthesis bifunctional protein argJ
B: Arginine biosynthesis bifunctional protein argJ
hetero molecules

A: Arginine biosynthesis bifunctional protein argJ
B: Arginine biosynthesis bifunctional protein argJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,46442
Polymers91,0934
Non-polymers2,37038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area24140 Å2
ΔGint-68 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.658, 70.658, 222.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Arginine biosynthesis bifunctional protein ... , 2 types, 2 molecules AB

#1: Protein Arginine biosynthesis bifunctional protein argJ


Mass: 22350.490 Da / Num. of mol.: 1 / Fragment: alpha chain, residues 1-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Description: both chain A and chain B were expressed from a single construct which encodes residues 1-411 of the ARGJ gene
Gene: argJ / Production host: Escherichia coli (E. coli)
References: UniProt: Q9K8V3, glutamate N-acetyltransferase, amino-acid N-acetyltransferase
#2: Protein Arginine biosynthesis bifunctional protein argJ


Mass: 23196.146 Da / Num. of mol.: 1 / Fragment: beta chain, residues 197-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Description: both chain A and chain B were expressed from a single construct which encodes residues 1-411 of the ARGJ gene
Gene: argJ / Production host: Escherichia coli (E. coli)
References: UniProt: Q9K8V3, glutamate N-acetyltransferase, amino-acid N-acetyltransferase

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Non-polymers , 4 types, 407 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.0559.62
22.8356.23
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop4.240.0% Ethylene-Glycol, 0.2M (NH4)2SO4, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop4.240.0% Ethylene-Glycol, 0.2M (NH4)2SO4, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.110.99187
SYNCHROTRONALS 8.2.120.97963, 0.99187, 0.97941
DetectorType: ADSC / Detector: CCD / Date: Jan 21, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.991871
20.979631
30.979411
ReflectionResolution: 2→29.81 Å / Num. obs: 38627 / % possible obs: 98.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 27.75 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21
Reflection shellResolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 10.2 / Num. unique all: 2387 / % possible all: 90.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA5.0)data scaling
SOLVEphasing
REFMAC5.2.0005refinement
Xpleorefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→29.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.1 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2) AN UNIDENTIFIABLE LIGAND, UNL, HAS BEEN MODELED INTO DENSITY NEAR RESIDUES A35-A37.
RfactorNum. reflection% reflectionSelection details
Rfree0.15782 1935 5 %RANDOM
Rwork0.13967 ---
obs0.14056 36636 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.334 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 84 388 3440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223135
X-RAY DIFFRACTIONr_bond_other_d0.0010.022882
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9624233
X-RAY DIFFRACTIONr_angle_other_deg0.83336709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78825.935123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65715508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.939159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
X-RAY DIFFRACTIONr_nbd_refined0.20.2610
X-RAY DIFFRACTIONr_nbd_other0.1710.22905
X-RAY DIFFRACTIONr_nbtor_other0.0850.21824
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.229
X-RAY DIFFRACTIONr_mcbond_it1.1171.52155
X-RAY DIFFRACTIONr_mcbond_other0.2191.5842
X-RAY DIFFRACTIONr_mcangle_it1.14623241
X-RAY DIFFRACTIONr_scbond_it2.48531208
X-RAY DIFFRACTIONr_scangle_it3.5814.5992
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1020.21
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.16 125 4.93 %
Rwork0.135 2413 -
obs--90.51 %
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)
11.1750.052-0.25160.3256-0.38470.8519-0.026-0.13650.02830.0294-0.00330.0692-0.0578-0.02820.0293-0.21980.00580.0111-0.11720.029-0.16728.598324.376280.0371
20.96570.494-0.2144.5951-0.36351.97010.0561-0.20320.03510.0374-0.1147-0.1447-0.28420.15880.0586-0.1978-0.04890.0217-0.12720.0032-0.227249.420538.962962.5222
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 19618 - 208
21BB197 - 2821 - 86
32BB283 - 40987 - 213

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