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- PDB-3if2: Crystal structure of Putative amino-acid aminotransferase (YP_265... -

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Basic information

Entry
Database: PDB / ID: 3if2
TitleCrystal structure of Putative amino-acid aminotransferase (YP_265399.1) from Psychrobacter arcticum 273-4 at 2.50 A resolution
ComponentsAminotransferase
KeywordsTRANSFERASE / YP_265399.1 / Putative amino-acid aminotransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aminotransferase
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesPsychrobacter arcticus 273-4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative amino-acid aminotransferase (YP_265399.1) from Psychrobacter arcticum 273-4 at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9407
Polymers99,2032
Non-polymers7385
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-61 kcal/mol
Surface area31470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.813, 152.813, 100.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain: (Details: A)
NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A0 - 401
1213B0 - 401
1314A402 - 407
1414B402 - 407
1516A408 - 443
1616B408 - 443
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Aminotransferase


Mass: 49601.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter arcticus 273-4 (bacteria)
Strain: DSM 17307 / 273-4 / Gene: avtA, Psyc_2118, YP_265399.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q4FPU3, Transferases; Transferring nitrogenous groups; Transaminases
#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.96 Å3/Da / Density % sol: 58.45 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1700M ammonium acetate, 15.0000% Glycerol, 25.5000% polyethylene glycol 4000, 0.1M sodium citrate pH 5.6, Additive: 0.001 M FeCl2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97934,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 20, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979341
30.97921
ReflectionResolution: 2.5→29.975 Å / Num. obs: 39646 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 3.79 % / Biso Wilson estimate: 47.923 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.5-2.590.4382136206839185.1
2.59-2.690.3692.5144917146193.5
2.69-2.810.2843.2149327354194.5
2.81-2.960.2164.1154967643194.7
2.96-3.150.1495.7156717727194.6
3.15-3.390.1067.7151147461195.2
3.39-3.730.06811.2150307445194.1
3.73-4.260.04315.6150697471195.1
4.26-5.350.0418.2151647510194.9
5.35-29.9750.03520.1155527709195.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.975 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 17.234 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.4 / ESU R Free: 0.245
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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. GLYCEROL (GOL) AND ACETATE (ACT) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. THE LIGAND PYRIDOXAL-5'-PHOSPHATE (PLP) IS MODELED INTO BOTH MONOMERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1986 5 %RANDOM
Rwork0.178 ---
obs0.181 39646 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.55 Å2 / Biso mean: 38.562 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6775 0 48 203 7026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227081
X-RAY DIFFRACTIONr_bond_other_d0.0030.024656
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9639644
X-RAY DIFFRACTIONr_angle_other_deg1.363311430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1085902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7525.227331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.166151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1051524
X-RAY DIFFRACTIONr_chiral_restr0.1070.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217987
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021393
X-RAY DIFFRACTIONr_mcbond_it0.80224400
X-RAY DIFFRACTIONr_mcbond_other0.13721783
X-RAY DIFFRACTIONr_mcangle_it1.37737090
X-RAY DIFFRACTIONr_scbond_it0.80622681
X-RAY DIFFRACTIONr_scangle_it1.30332539
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A2311TIGHT POSITIONAL0.180.05
B74MEDIUM POSITIONAL0.920.5
A3216LOOSE POSITIONAL0.285
B2311TIGHT THERMAL1.220.5
A74MEDIUM THERMAL6.532
B3216LOOSE THERMAL1.4210
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 148 -
Rwork0.243 2686 -
all-2834 -
obs--96.43 %
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)
10.8688-0.55920.03550.884-0.32271.6135-0.1603-0.1368-0.05040.21820.0582-0.07670.03370.10980.10210.07220.0348-0.0250.03780.00480.045326.90860.60876.081
21.1818-0.4552-0.08320.6914-0.17021.775-0.04010.2488-0.0418-0.0767-0.0742-0.13140.0590.17370.11440.0197-0.00790.02250.0792-0.0150.063321.46953.68141.716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 132
2X-RAY DIFFRACTION1A140 - 443
3X-RAY DIFFRACTION2B0 - 132
4X-RAY DIFFRACTION2B140 - 443

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