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- PDB-3f0h: Crystal structure of Aminotransferase (RER070207000802) from Euba... -

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Basic information

Entry
Database: PDB / ID: 3f0h
TitleCrystal structure of Aminotransferase (RER070207000802) from Eubacterium rectale at 1.70 A resolution
ComponentsAminotransferase
KeywordsTRANSFERASE / RER070207000802 / Aminotransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aminotransferase class-V
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 speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Aminotransferase (RER070207000802) from Eubacterium rectale at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
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 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2475
Polymers42,9711
Non-polymers2764
Water6,792377
1
A: Aminotransferase
hetero molecules

A: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,49410
Polymers85,9422
Non-polymers5538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area7740 Å2
ΔGint-10 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.450, 62.450, 373.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Aminotransferase


Mass: 42970.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Gene: RER070207000802 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97966
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979661
ReflectionResolution: 1.7→29.617 Å / Num. obs: 49360 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 20.28 % / Biso Wilson estimate: 23.322 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.56
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.761.2921.79726938745198.3
1.76-1.831.0282.8972368912199.6
1.83-1.910.7314982428647199.7
1.91-2.020.46961124169826199.6
2.02-2.140.2958.9973408483199.8
2.14-2.310.2111.81068469267199.9
2.31-2.540.15715.11020078824199.9
2.54-2.90.11120.11027808867199.9
2.9-3.660.07328.51061569127199.9
3.66-29.620.058361051519063199.6

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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: 1.7→29.617 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.394 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.078
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. PLP IS COVALENTLY ATTACHED TO LYS187 (LLP). RESIDUAL DENSITY SUGGESTS ADDITIONAL MOIETY MAY BE ATTACHED TO THE C4A ATOM OF PLP. THESE DENSITIES ARE MODELED AS AN UNKNOWN LIGAND (UNL). 5. GLYCEROL MODELED ARE PRESENT IN CRYO CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 2495 5.1 %RANDOM
Rwork0.147 ---
obs0.148 49180 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.51 Å2 / Biso mean: 22.138 Å2 / Biso min: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.52 Å20 Å2
2--1.03 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 25 377 3225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223035
X-RAY DIFFRACTIONr_bond_other_d0.0010.022062
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9784134
X-RAY DIFFRACTIONr_angle_other_deg0.89435090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67925.111135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93815548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.021513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02591
X-RAY DIFFRACTIONr_mcbond_it1.45331871
X-RAY DIFFRACTIONr_mcbond_other0.4513757
X-RAY DIFFRACTIONr_mcangle_it2.40253052
X-RAY DIFFRACTIONr_scbond_it4.02381164
X-RAY DIFFRACTIONr_scangle_it6.202111058
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 199 -
Rwork0.26 3317 -
all-3516 -
obs--98.35 %
Refinement TLS params.Method: refined / Origin x: 2.3974 Å / Origin y: 42.6825 Å / Origin z: 15.6357 Å
111213212223313233
T0.0329 Å20.014 Å2-0.0087 Å2-0.0072 Å2-0.0061 Å2--0.0075 Å2
L0.2361 °2-0.1082 °2-0.0536 °2-0.3718 °20.1946 °2--0.8271 °2
S0.0141 Å °0.0025 Å °0.0046 Å °-0.0853 Å °-0.0362 Å °0.0292 Å °-0.1409 Å °-0.0578 Å °0.0221 Å °

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