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- PDB-3gju: Crystal structure of a putative aminotransferase (mll7127) from m... -

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Basic information

Entry
Database: PDB / ID: 3gju
TitleCrystal structure of a putative aminotransferase (mll7127) from mesorhizobium loti maff303099 at 1.55 A resolution
ComponentsPutative aminotransferaseTransaminase
KeywordsTRANSFERASE / Pyridoxal phosphate / plp-dependent transferase-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
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 ...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 / Putative aminotransferase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative aminotransferase (NP_107505.1) from Mesorhizobium loti at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: 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: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9424
Polymers50,4581
Non-polymers4833
Water8,251458
1
A: Putative aminotransferase
hetero molecules

A: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8838
Polymers100,9162
Non-polymers9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10750 Å2
ΔGint-74.6 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.224, 59.577, 85.337
Angle α, β, γ (deg.)90.000, 130.590, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-496-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THAT A DIMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein Putative aminotransferase / Transaminase


Mass: 50458.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mll7127, NP_107505.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q987B2
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: NANODROP, 59.1% 2-methyl-2,4-pentanediol, 0.1M Bicine pH 8.0, 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: 0.91162, 0.97941, 0.97954
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 18, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979411
30.979541
ReflectionResolution: 1.55→28.33 Å / Num. obs: 61448 / % possible obs: 92 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.794 Å2 / Rmerge(I) obs: 0.057
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.55-1.610.521.51423811275185.2
1.61-1.670.4181.91307710381190.7
1.67-1.750.3372.41484211791191.2
1.75-1.840.2333.31370510954191.9
1.84-1.950.1654.61362810919192.5
1.95-2.10.1026.71430011479192.9
2.1-2.310.0679.71434411566193.3
2.31-2.650.05212.21471811856194.2
2.65-3.330.03218.31430111558194.2
3.33-28.330.01828.81462611810194.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.55→28.33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.26 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.07
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. 2-METHYL-2,4-PENTANEDIOL (MPD) FROM THE CRYSTALLIZATION CONDITION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 5. PYRIDOXAL PHOSPHATE IN DUAL CONFORMATION AS FREE PLP AND COVALENTLY ATTACHED TO LYS289 (LLP) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON DIFFERENCE DENSITY AND OMIT MAPS AND STRUCTURAL SIMILARITY TO PLP-DEPENDENT AMINOTRANSFERASES. 6. RESIDUE ALA288 IS PRESENT IN THE VICINITY OF THE PUTATIVE ACTIVE SITE AND IS A RAMACHANDRAN OUTLIER. THIS COULD HAVE SOME FUNCTIONAL SIGNIFICANCE.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 3122 5.1 %RANDOM
Rwork0.139 ---
obs0.14 61444 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.16 Å2 / Biso mean: 14.405 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å2-0.49 Å2
2--1.33 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 32 458 3977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223697
X-RAY DIFFRACTIONr_bond_other_d0.0010.022459
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9635043
X-RAY DIFFRACTIONr_angle_other_deg0.9936008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83323.742155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.411521
X-RAY DIFFRACTIONr_chiral_restr0.0980.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02757
X-RAY DIFFRACTIONr_mcbond_it1.45332311
X-RAY DIFFRACTIONr_mcbond_other0.4713965
X-RAY DIFFRACTIONr_mcangle_it2.14153709
X-RAY DIFFRACTIONr_scbond_it3.72381386
X-RAY DIFFRACTIONr_scangle_it5.059111318
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 227 -
Rwork0.248 4065 -
all-4292 -
obs--94.62 %
Refinement TLS params.Method: refined / Origin x: 17.4846 Å / Origin y: 18.6939 Å / Origin z: 21.9808 Å
111213212223313233
T0.0055 Å20.001 Å20.0047 Å2-0.0149 Å20.0056 Å2--0.0117 Å2
L0.2474 °20.0717 °20.098 °2-0.1991 °2-0.0059 °2--0.2405 °2
S-0.0195 Å °0.0212 Å °-0.0061 Å °-0.0213 Å °0.0229 Å °0.0066 Å °-0.0128 Å °-0.0289 Å °-0.0034 Å °

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