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- PDB-1vp4: Crystal structure of a putative aminotransferase (tm1131) from th... -

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Basic information

Entry
Database: PDB / ID: 1vp4
TitleCrystal structure of a putative aminotransferase (tm1131) from thermotoga maritima msb8 at 1.82 A resolution
Componentsaminotransferase, putativeTransaminase
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


alpha-amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
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 ...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
FORMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Unknown ligand / Aminotransferase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.82 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Aminotransferase, putative (TM1131) from Thermotoga maritima at 1.82 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: aminotransferase, putative
B: aminotransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,27039
Polymers98,1602
Non-polymers2,10937
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-30 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.125, 165.125, 68.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 413 / Label seq-ID: 13 - 425

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein aminotransferase, putative / Transaminase


Mass: 49080.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L5

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Non-polymers , 5 types, 390 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.: 2 / Source method: obtained synthetically
#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: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 20.0% PEG-3350, 0.2M NaFormate, 2.0mM n-Dodecyl-beta-D-maltoside, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.110.9794
SYNCHROTRONALS 8.2.121.0000,0.9796
DetectorType: ADSC / Detector: CCD / Date: Aug 4, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
211
30.97961
ReflectionResolution: 1.82→28.41 Å / Num. obs: 94227 / % possible obs: 98.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 36.02 Å2 / Rsym value: 0.054 / Net I/σ(I): 13.8
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 12449 / Rsym value: 0.418 / % possible all: 89.3

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Processing

Software
NameVersionClassification
XDSautodata collection
SCALA4.2)data scaling
SHELXmodel building
SHARPphasing
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.82→28.41 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.065 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.107
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS POOR DENSITY REGION AT B16-20. UNKNOWN LIGANDS MODELED NEAR PLP IN EACH MONOMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.20341 4716 5 %RANDOM
Rwork0.17902 ---
obs0.18022 89425 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.428 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.82→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 148 353 7036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226817
X-RAY DIFFRACTIONr_bond_other_d0.0020.026361
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9919186
X-RAY DIFFRACTIONr_angle_other_deg0.877314704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5655834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71423.895285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.992151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.091538
X-RAY DIFFRACTIONr_chiral_restr0.0920.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021362
X-RAY DIFFRACTIONr_nbd_refined0.2240.21505
X-RAY DIFFRACTIONr_nbd_other0.1930.26582
X-RAY DIFFRACTIONr_nbtor_other0.0890.23884
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2355
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.27
X-RAY DIFFRACTIONr_mcbond_it2.22634334
X-RAY DIFFRACTIONr_mcbond_other0.61731721
X-RAY DIFFRACTIONr_mcangle_it2.80156738
X-RAY DIFFRACTIONr_scbond_it5.41782798
X-RAY DIFFRACTIONr_scangle_it7.386112448
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23455
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2420.21
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 6287 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.360.5
medium thermal0.962
LS refinement shellResolution: 1.82→1.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 286 4.8 %
Rwork0.3 5671 -
obs--84.04 %
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)
10.40160.32120.07820.760.05310.2549-0.06090.0489-0.001-0.09650.04440.1035-0.0374-0.07710.0165-0.1634-0.0328-0.0032-0.20210.0111-0.2628-27.412117.8768.002
20.46210.0443-0.01360.84490.15270.5786-0.0661-0.06410.06460.12180.02210.0923-0.0975-0.09390.044-0.12310.0195-0.0146-0.20410.0158-0.2664-20.947142.10531.673
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 413 / Label seq-ID: 13 - 425

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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