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- PDB-2ord: Crystal structure of Acetylornithine aminotransferase (EC 2.6.1.1... -

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Basic information

Entry
Database: PDB / ID: 2ord
TitleCrystal structure of Acetylornithine aminotransferase (EC 2.6.1.11) (ACOAT) (TM1785) from Thermotoga maritima at 1.40 A resolution
ComponentsAcetylornithine aminotransferase
KeywordsTRANSFERASE / TM1785 / Acetylornithine aminotransferase (EC 2.6.1.11) (ACOAT) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / L-arginine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Acetylornithine/Succinylornithine transaminase family / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Acetylornithine/Succinylornithine transaminase family / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Acetylornithine aminotransferase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Acetylornithine aminotransferase (EC 2.6.1.11) (ACOAT) (TM1785) from Thermotoga maritima at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,79521
Polymers89,7352
Non-polymers2,06019
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15570 Å2
ΔGint-92 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.948, 95.628, 96.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA-6 - 3856 - 397
21ILEILEBB-6 - 3856 - 397
32PLPPLPAC4011
42PLPPLPBD4011
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Acetylornithine aminotransferase / ACOAT


Mass: 44867.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8, DSM 3109, JCM 10099 / Gene: argD, TM1785 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9X2A5, acetylornithine transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 1.6M Sodium citrate, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97937, 0.97876
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979371
30.978761
ReflectionResolution: 1.4→42.796 Å / Num. obs: 137451 / % possible obs: 82.3 % / Biso Wilson estimate: 17.75 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.4-1.450.4542.112656546133.5
1.45-1.510.4132.521624843650.1
1.51-1.580.3682.9299801090365.9
1.58-1.660.333.6424491413190.2
1.66-1.760.274.5478461527896.5
1.76-1.90.196.2513141642697.1
1.9-2.090.1149.9498781598097.5
2.09-2.390.0714.8502031612198
2.390.04819.8508801638898.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→42.796 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.368 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PLP MONOMERS ARE MODELED BASED ON DENSITY AND STRUCTURAL HOMOLOGS. OCCUPANCIES OF PLP (0.8) ARE ASSIGNED BASED ON DIFFERENCE MAPS. GOL ARE FROM CRYOPROTECTANT. 5. RAMACHANDRAN OUTLIERS A239 AND B239 ARE SUPPORTED BY DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17 6909 5 %RANDOM
Rwork0.148 ---
all0.149 ---
obs0.149 137417 84.15 %-
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: 14.058 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6136 0 132 670 6938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226586
X-RAY DIFFRACTIONr_bond_other_d0.0010.025993
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9788913
X-RAY DIFFRACTIONr_angle_other_deg0.826314006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39824.551301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.298151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9491531
X-RAY DIFFRACTIONr_chiral_restr0.0890.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021312
X-RAY DIFFRACTIONr_nbd_refined0.2190.21309
X-RAY DIFFRACTIONr_nbd_other0.180.26130
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23225
X-RAY DIFFRACTIONr_nbtor_other0.0840.23546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0580.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.254
X-RAY DIFFRACTIONr_mcbond_it1.90234265
X-RAY DIFFRACTIONr_mcbond_other0.47531648
X-RAY DIFFRACTIONr_mcangle_it2.26656428
X-RAY DIFFRACTIONr_scbond_it3.76872836
X-RAY DIFFRACTIONr_scangle_it5.0472455
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5776 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.250.5
MEDIUM THERMAL0.572
LS refinement shellResolution: 1.4→1.441 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 221 -
Rwork0.359 4199 -
obs-4420 36.96 %
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)
10.1653-0.0029-0.00480.2893-0.00380.1993-0.0311-0.0075-0.0242-0.00630.02190.02810.0324-0.03550.0093-0.02-0.00670.0003-0.01190.0039-0.018525.465141.364726.0059
20.20920.0302-0.01580.3084-0.01710.1837-0.0262-0.00890.0380.00980.0230.029-0.0311-0.03650.0032-0.01540.0098-0.0045-0.01140.0017-0.020625.570570.329927.5314
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: -7 - 385 / Label seq-ID: 5 - 397

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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