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- PDB-3csw: Crystal structure of a putative branched-chain amino acid aminotr... -

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Basic information

Entry
Database: PDB / ID: 3csw
TitleCrystal structure of a putative branched-chain amino acid aminotransferase (TM0831) from Thermotoga maritima at 2.15 A resolution
ComponentsPutative branched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / TM0831 / Putative Branched-Chain Amino Acid Aminotransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis / Pyridoxal phosphate
Function / homology
Function and homology information


branched-chain-amino-acid transaminase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / cytosol
Similarity search - Function
Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / 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 ...Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / 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
CITRIC ACID / PYRIDOXAL-5'-PHOSPHATE / Unknown ligand / Probable branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative Branched-Chain Amino Acid Aminotransferase (TM0831) from Thermotoga maritima at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 branched-chain-amino-acid aminotransferase
B: Putative branched-chain-amino-acid aminotransferase
C: Putative branched-chain-amino-acid aminotransferase
D: Putative branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,08824
Polymers131,0484
Non-polymers2,04020
Water11,187621
1
A: Putative branched-chain-amino-acid aminotransferase
B: Putative branched-chain-amino-acid aminotransferase
hetero molecules

A: Putative branched-chain-amino-acid aminotransferase
B: Putative branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,39826
Polymers131,0484
Non-polymers2,35022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area10360 Å2
ΔGint-49.4 kcal/mol
Surface area40980 Å2
MethodPISA
2
C: Putative branched-chain-amino-acid aminotransferase
D: Putative branched-chain-amino-acid aminotransferase
hetero molecules

C: Putative branched-chain-amino-acid aminotransferase
D: Putative branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,77722
Polymers131,0484
Non-polymers1,72918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Buried area10340 Å2
ΔGint-55.9 kcal/mol
Surface area41790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.710, 129.760, 298.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11C-481-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13A
23C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISILE4AA0 - 27312 - 285
21HISILE4CC0 - 27312 - 285
12HISILE4BB0 - 27312 - 285
22HISILE4DD0 - 27312 - 285
13PLPPLP1AI3001
23PLPPLP1CN3001

NCS ensembles :
ID
1
2
3
DetailsSIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative branched-chain-amino-acid aminotransferase / BCAT


Mass: 32761.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM0831, ilvE / Plasmid: MH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: P74921, branched-chain-amino-acid transaminase

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Non-polymers , 6 types, 641 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A PRESENCE OF VALINE AT POSITION 1 WHEN EXPRESSED AS A FUSION WITH THE PURIFICATION TAG.

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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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.03
Details: NANODROP, 52.0% 2-methyl-2,4-pentanediol, 0.1M Citric acid pH 4.03, 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, 0.97961, 0.97975
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2008 / 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
20.979611
30.979751
ReflectionResolution: 2.15→29.748 Å / Num. obs: 111860 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.759 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.94
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.230.6571.24067621162192.5
2.23-2.320.5471.54238221866198.9
2.32-2.420.4321.94022520646199
2.42-2.550.3122.64322822103198.6
2.55-2.710.2273.74255021676198.4
2.71-2.920.16454282621685198.2
2.92-3.210.10284212821249197.8
3.21-3.670.05513.94263421343197.3
3.67-4.610.03222.94276921196196.5
4.61-29.7480.02429.14323321163194.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.748 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.471 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.133
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. DENSITY FOR LOOP RESIDUES A/B/C/D 59-62 IS POOR. 4. CITRATE, CL, MPD MOLECULES FROM ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. DENSITY FOR LOOP RESIDUES A/B/C/D 59-62 IS POOR. 4. CITRATE, CL, MPD MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. RESIDUAL DENSITIES IN THE ACTIVE SITES WERE MODELED AS UNKNOWN LIGANDS (UNL).
RfactorNum. reflection% reflectionSelection details
Rfree0.2 5612 5 %RANDOM
Rwork0.167 ---
obs0.168 111840 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--1.11 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8737 0 145 621 9503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229215
X-RAY DIFFRACTIONr_bond_other_d0.0020.026267
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.98312576
X-RAY DIFFRACTIONr_angle_other_deg1.029315247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14451136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40523.446415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.186151534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3181568
X-RAY DIFFRACTIONr_chiral_restr0.0970.21432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021953
X-RAY DIFFRACTIONr_nbd_refined0.1990.21536
X-RAY DIFFRACTIONr_nbd_other0.1950.26338
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24342
X-RAY DIFFRACTIONr_nbtor_other0.0830.24696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2517
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1740.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.220
X-RAY DIFFRACTIONr_mcbond_it1.85935752
X-RAY DIFFRACTIONr_mcbond_other0.51632219
X-RAY DIFFRACTIONr_mcangle_it2.93159066
X-RAY DIFFRACTIONr_scbond_it4.71983968
X-RAY DIFFRACTIONr_scangle_it6.78113490
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3655MEDIUM POSITIONAL0.250.5
1A3655MEDIUM THERMAL0.92
2B3618MEDIUM POSITIONAL0.280.5
2B3618MEDIUM THERMAL0.922
3A20TIGHT POSITIONAL0.020.05
3A20TIGHT THERMAL0.150.5
LS refinement shellResolution: 2.15→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 401 -
Rwork0.257 7542 -
all-7943 -
obs--95.33 %
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)
10.7244-0.09840.26841.224-0.16791.22870.05580.0536-0.0748-0.19-0.00630.2070.1518-0.1589-0.0495-0.0502-0.0183-0.0590.03770.0006-0.051131.872921.265120.6444
21.66530.1153-0.16380.4988-0.1560.3973-0.0011-0.2175-0.30460.068-0.0234-0.04850.08370.06650.0245-0.03090.0226-0.0307-0.01420.0757-0.020254.45277.445343.9161
30.79570.1432-0.43310.3467-0.09481.05230.04960.05260.11570.0375-0.02140.0009-0.04430.0614-0.0282-0.0681-0.01560.0216-0.0720.0294-0.027315.295321.278563.1321
41.29080.05690.42360.7665-0.48771.01370.03370.19590.084-0.09280.04230.14460.04760.0606-0.076-0.04030.0202-0.0343-0.06190.03-0.0571-8.4399-1.320749.7294
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 27312 - 285
2X-RAY DIFFRACTION1AI3001
3X-RAY DIFFRACTION2BB0 - 27312 - 285
4X-RAY DIFFRACTION3CC-1 - 27311 - 285
5X-RAY DIFFRACTION3CN3001
6X-RAY DIFFRACTION4DD0 - 27312 - 285

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