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- PDB-3op7: Crystal structure of a PLP-dependent aminotransferase (ZP_0362512... -

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Basic information

Entry
Database: PDB / ID: 3op7
TitleCrystal structure of a PLP-dependent aminotransferase (ZP_03625122.1) from Streptococcus suis 89-1591 at 1.70 A resolution
ComponentsAminotransferase class I and II
KeywordsTRANSFERASE / PLP-DEPENDENT TRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / Unknown ligand / :
Function and homology information
Biological speciesStreptococcus suis 89/1591 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a PLP-dependent aminotransferase (ZP_03625122.1) from Streptococcus suis 89-1591 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 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: Aminotransferase class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,70011
Polymers43,0401
Non-polymers66110
Water4,990277
1
A: Aminotransferase class I and II
hetero molecules

A: Aminotransferase class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,40122
Polymers86,0792
Non-polymers1,32120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10040 Å2
ΔGint-73 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.518, 97.518, 89.244
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Aminotransferase class I and II


Mass: 43039.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis 89/1591 (bacteria) / Gene: SsuiDRAFT_2941 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B9WVA1
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.20M lithium sulfate, 2.00M ammonium sulfate, Additive: 0.001M pyridoxal 5'-phosphate (PLP), 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: 0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.7→29.748 Å / Num. all: 47906 / Num. obs: 47906 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 24.986 Å2 / Rsym value: 0.087 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.747.30.920.82555235050.92100
1.74-1.797.30.671.22465733720.67100
1.79-1.847.30.5481.42421733090.548100
1.84-1.97.30.4161.92360732160.416100
1.9-1.967.30.3122.52292831220.312100
1.96-2.037.30.25132235830570.251100
2.03-2.117.40.2043.72126028860.204100
2.11-2.197.30.164.62060628080.16100
2.19-2.297.30.1385.11987527090.138100
2.29-2.47.40.125.71914626020.12100
2.4-2.537.40.1175.71816124680.117100
2.53-2.697.30.1145.71719923490.114100
2.69-2.877.30.1056.11627822280.105100
2.87-3.17.30.08971496920450.089100
3.1-3.47.30.0728.41396219170.072100
3.4-3.87.20.0639.61260717420.063100
3.8-4.397.20.05910.11120215580.059100
4.39-5.387.10.05610.5943913360.056100
5.38-7.66.90.06210.2725710590.062100
7.6-29.7486.20.05311.738226180.05397.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.748 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.15 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. SULFATE (SO4) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 7. RESIDUE LYSINE 221 IS COVALENTLY ATTACHED TO PYRIDOXAL-5'-PHOSPHATE VIA SCHIFF BASE LINKAGE AND IS MODELED AS LLP. 8. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED NEAR RESIDUE LLP 221. THE UNL RESEMBLES PYRIDOXAMINE (PXM), A POSSIBLE REACTION PRODUCT OF THE ENZYME.
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 2423 5.1 %RANDOM
Rwork0.1636 ---
obs0.1653 47834 99.96 %-
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: 86.44 Å2 / Biso mean: 35.7562 Å2 / Biso min: 17.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å20 Å2
2---1.69 Å20 Å2
3---3.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 51 277 3295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223187
X-RAY DIFFRACTIONr_bond_other_d0.0010.022130
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9884351
X-RAY DIFFRACTIONr_angle_other_deg0.98435225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67124.967153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99515547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.351517
X-RAY DIFFRACTIONr_chiral_restr0.0990.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213533
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
X-RAY DIFFRACTIONr_mcbond_it0.8311.51900
X-RAY DIFFRACTIONr_mcbond_other0.2721.5768
X-RAY DIFFRACTIONr_mcangle_it1.3823095
X-RAY DIFFRACTIONr_scbond_it2.34431287
X-RAY DIFFRACTIONr_scangle_it3.6514.51240
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 192 -
Rwork0.248 3300 -
all-3492 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 29.511 Å / Origin y: 28.9 Å / Origin z: 16.407 Å
111213212223313233
T0.1793 Å2-0.0185 Å20.0279 Å2-0.114 Å2-0.0261 Å2--0.0143 Å2
L0.9197 °20.4003 °2-0.2521 °2-1.417 °2-0.3286 °2--1.2996 °2
S0.0948 Å °-0.1602 Å °0.0801 Å °0.3108 Å °-0.0408 Å °0.1118 Å °-0.0716 Å °0.0356 Å °-0.054 Å °

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