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- PDB-3sno: Crystal structure of a putative aminotransferase (NCgl2491) from ... -

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Basic information

Entry
Database: PDB / ID: 3sno
TitleCrystal structure of a putative aminotransferase (NCgl2491) from Corynebacterium glutamicum ATCC 13032 at 1.60 A resolution
ComponentsHypothetical aminotransferase
KeywordsTRANSFERASE / D-aminoacid aminotransferase-like PLP-dependent enzymes / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / lyase activity
Similarity search - Function
Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel ...Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical aminotransferase (NCgl2491) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4334
Polymers34,2471
Non-polymers1863
Water3,369187
1
A: Hypothetical aminotransferase
hetero molecules

A: Hypothetical aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8678
Polymers68,4942
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2170 Å2
ΔGint-8 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.899, 52.586, 37.350
Angle α, β, γ (deg.)90.000, 98.920, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY IN COMBINATION WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Hypothetical aminotransferase / Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase


Mass: 34247.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 KITASATO / Gene: Cgl2580 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: Q8NMJ3, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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: 1.98 Å3/Da / Density % sol: 37.93 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.64
Details: 10.0% 2-methyl-2,4-pentanediol, 0.1M citric acid pH 3.64, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97949,0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979491
30.979321
ReflectionResolution: 1.6→28.757 Å / Num. obs: 34491 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.711 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 12.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.660.4561.77588573679.5
1.66-1.720.37727739574391.5
1.72-1.80.23338879660192.2
1.8-1.90.1454.69136679793.3
1.9-2.020.0767.78778656893.5
2.02-2.170.0511.28305624094.4
2.17-2.390.035158870668495.3
2.39-2.730.02719.78591649795.2
2.73-3.440.01926.48912674396.2
3.440.01831.38533651593

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 30, 2009data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.6→28.757 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9227 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. 1,2 ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 4. RAMACHANDRAN OUTLIER AT RESIDUE 294 IS IN A REGION OF SUB-OPTIMAL ELECTRON DENSITY. 5. THE STRUCTURE HAS SEVERAL UNMODELED REGIONS WHICH HAVE ELECTRON DENSITY THAT COULD NOT BE RELIABLY INTERPRETED. IN ADDITION, THERE ARE THREE REGIONS OF SUB-OPTIMAL MODEL FIT IN WHICH THE MOST STRUCTURALLY SIMILAR PROTEIN (AS DETERMINED BY THE PROGRAM SSM), PDB ID 5DAA, WAS USED TO GUIDE THE MODELING. THESE INCLUDE RESIDUES 143-150, 204-221 AND 291-295. 6. THE REFINEMENT WAS RESTRAINED WITH THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 1737 5.04 %RANDOM
Rwork0.2309 ---
obs0.232 34490 --
Displacement parametersBiso max: 111.64 Å2 / Biso mean: 38.1043 Å2 / Biso min: 16.99 Å2
Baniso -1Baniso -2Baniso -3
1-6.6766 Å20 Å2-0.3661 Å2
2---7.1797 Å20 Å2
3---0.5031 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 12 187 2033
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d956SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes315HARMONIC5
X-RAY DIFFRACTIONt_it1996HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion274SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2391SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1996HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2729HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion2.52
LS refinement shellResolution: 1.6→1.65 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2314 111 4.2 %
Rwork0.2342 2535 -
all0.234 2646 -
Refinement TLS params.Method: refined / Origin x: 51.3026 Å / Origin y: 35.0874 Å / Origin z: -3.323 Å
111213212223313233
T-0.1001 Å20.004 Å20.0097 Å2--0.0982 Å20.0178 Å2---0.0445 Å2
L1.7657 °21.0792 °2-0.1063 °2-1.6581 °2-0.0924 °2--0.5035 °2
S-0.1551 Å °0.0186 Å °-0.1213 Å °-0.2014 Å °0.0473 Å °-0.0408 Å °0.0754 Å °-0.0052 Å °0.1078 Å °
Refinement TLS groupSelection details: { A|10 - A|314 }

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