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- PDB-3p1t: Crystal structure of a putative aminotransferase (BPSL1724) from ... -

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Basic information

Entry
Database: PDB / ID: 3p1t
TitleCrystal structure of a putative aminotransferase (BPSL1724) from Burkholderia pseudomallei K96243 at 2.60 A resolution
ComponentsPutative histidinol-phosphate aminotransferase
KeywordsTRANSFERASE / PLP-DEPENDENT TRANSFERASE-LIKE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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
L(+)-TARTARIC ACID / Aminotransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative aminotransferase (BPSL1724) from Burkholderia pseudomallei K96243 at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
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: Putative histidinol-phosphate aminotransferase
B: Putative histidinol-phosphate aminotransferase
C: Putative histidinol-phosphate aminotransferase
D: Putative histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,22726
Polymers150,2864
Non-polymers1,94222
Water10,233568
1
A: Putative histidinol-phosphate aminotransferase
B: Putative histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,16614
Polymers75,1432
Non-polymers1,02312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-39 kcal/mol
Surface area24950 Å2
MethodPISA
2
C: Putative histidinol-phosphate aminotransferase
D: Putative histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,06212
Polymers75,1432
Non-polymers91910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-11 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.550, 167.550, 290.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11D-839-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Putative histidinol-phosphate aminotransferase


Mass: 37571.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BPSL1724 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q63U92
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 277 K / pH: 9.25
Details: 0.20M lithium sulfate, 0.90M potassium sodium tartrate, 0.1M CHES pH 9.25, Additive, 0.005 M alpha ketoglutaric acid, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936,0.97922
DetectorType: MAR MAR325 / Detector: CCD / Date: May 12, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
30.979221
ReflectionResolution: 2.6→29.647 Å / Num. obs: 62018 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.45 Å2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.144 / Mean I/σ(I) obs: 1.6 / % possible all: 93.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→29.65 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.33
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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. SULFATE (SO4) AND L(+)-TARTARIC ACID (TLA) FROM THE CRYSTALLIZATION SOLUTION AND ETHYLENE GLYCOL USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflection
Rfree0.234 3131 5.05 %
Rwork0.2 --
obs0.202 61978 -
Displacement parametersBiso mean: 43.03 Å2
Baniso -1Baniso -2Baniso -3
1--3.9754 Å20 Å20 Å2
2---3.9754 Å20 Å2
3---7.9507 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9960 0 121 568 10649
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4894SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes284HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1565HARMONIC5
X-RAY DIFFRACTIONt_it10346HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1294SEMIHARMONIC5
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_contact11608SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10346HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13960HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion2.48
LS refinement shellResolution: 2.6→2.67 Å
RfactorNum. reflection% reflection
Rfree0.2199 196 4.64 %
Rwork0.2023 4028 -
all0.2031 4224 -
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)
10.88450.284-0.14830.7992-0.16051.3010.0219-0.3075-0.16980.0407-0.0599-0.03940.1817-0.05950.038-0.1328-0.0046-0.02610.10490.0766-0.165589.86-20.326134.4252
20.9896-0.1390.44290.36460.0720.57470.0347-0.04020.0093-0.0097-0.0276-0.0386-0.02430.0997-0.007-0.11410.0116-0.00840.10690.0063-0.1061111.4580.69514.8347
30.93140.17480.14690.78610.14031.3061-0.03480.08560.0234-0.13910.01630.079-0.0484-0.2580.0185-0.10420.0255-0.03530.01410.0226-0.112763.64416.5095-38.9527
40.30960.0208-0.06880.8142-0.22031.1515-0.0109-0.01760.03570.06010.0118-0.0169-0.34320.0506-0.00090.03670.0043-0.0008-0.08310.0065-0.086984.530127.4986-19.3189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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