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- PDB-1vlo: Crystal structure of aminomethyltransferase (T protein; tetrahydr... -

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Basic information

Entry
Database: PDB / ID: 1vlo
TitleCrystal structure of aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system (np417381) from Escherichia coli k12 at 1.70 A resolution
ComponentsAminomethyltransferase
KeywordsTRANSFERASE / np417381 / aminomethyltransferase (T protein / tetrahydrofolate-dependent) of glycine cleavage system / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


aminomethyltransferase / aminomethyltransferase activity / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / transaminase activity / one-carbon metabolic process / cytosol
Similarity search - Function
Glycine cleavage system T protein, bacteria / Aminomethyltransferase fragment / Aminomethyltransferase fragment / Glycine cleavage system T protein / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 ...Glycine cleavage system T protein, bacteria / Aminomethyltransferase fragment / Aminomethyltransferase fragment / Glycine cleavage system T protein / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / Gyrase A; domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Few Secondary Structures / Irregular / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aminomethyltransferase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system (np417381) from Escherichia coli k12 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Remark 999SEQUENCE FIVE EXTRA AMINO ACID RESIDUES (GLY,LEU,CYS,GLY AND ARG) WERE ENGINEERED INTO THE C- ...SEQUENCE FIVE EXTRA AMINO ACID RESIDUES (GLY,LEU,CYS,GLY AND ARG) WERE ENGINEERED INTO THE C-TERMINUS OF PROTEIN CHAIN DUE TO THE CONSTRUCT DESIGN IN GENE CLONING PROCESS. ONLY THREE RESIDUES (GLY,LEU AND CYS) OF THESE WERE OBSERVED IN THE DENSITY AND INCLUDED IN THE MODEL. THE N-TERMINAL MET OF THE PROTEIN (NOT INCLUDING THE HIS-TAG LINKER) IS REMOVED FROM THE PROTEIN DUE TO THE CONSTRUCT DESIGN FOR GENE CLONING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminomethyltransferase


Theoretical massNumber of molelcules
Total (without water)42,7111
Polymers42,7111
Non-polymers00
Water7,548419
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.517, 64.564, 117.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminomethyltransferase / / Glycine cleavage system T protein


Mass: 42711.320 Da / Num. of mol.: 1 / Mutation: 2.1.2.10
Source method: isolated from a genetically manipulated source
Details: T protein, tetrahydrofolate-dependent / Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: k12 / Gene: gcvT / Production host: Escherichia coli (E. coli) / References: UniProt: P27248, aminomethyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 1.93 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 20.0% PEG-10000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
MAD1
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-110.885567
SYNCHROTRONSSRL BL11-120.979048,0.979494, 0.885567
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2004 / Details: flat mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.8855671
20.9790481
30.9794941
ReflectionResolution: 1.7→43.38 Å / Num. obs: 38018 / % possible obs: 96.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2326 / Rsym value: 0.389 / % possible all: 81.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→43.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.757 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.103
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19514 1920 5.1 %RANDOM
Rwork0.15872 ---
obs0.16051 36059 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.94 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 0 419 3219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222897
X-RAY DIFFRACTIONr_bond_other_d0.0020.022645
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9363933
X-RAY DIFFRACTIONr_angle_other_deg0.79836120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1235373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25723.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34715477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.351521
X-RAY DIFFRACTIONr_chiral_restr0.0790.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023302
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_nbd_refined0.2130.2535
X-RAY DIFFRACTIONr_nbd_other0.1860.22739
X-RAY DIFFRACTIONr_nbtor_other0.0820.21765
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.220
X-RAY DIFFRACTIONr_mcbond_it1.81131930
X-RAY DIFFRACTIONr_mcbond_other0.423761
X-RAY DIFFRACTIONr_mcangle_it2.24452933
X-RAY DIFFRACTIONr_scbond_it4.17481170
X-RAY DIFFRACTIONr_scangle_it5.419111000
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 134 5.78 %
Rwork0.19 2185 -
Refinement TLS params.Method: refined / Origin x: 33.0072 Å / Origin y: 31.1459 Å / Origin z: 5.7922 Å
111213212223313233
T-0.0415 Å2-0.0032 Å20.0035 Å2--0.0516 Å20.0057 Å2---0.0539 Å2
L0.3569 °20.0607 °20.1319 °2-0.7287 °2-0.048 °2--0.3645 °2
S0.0245 Å °0.0316 Å °0.0161 Å °-0.0252 Å °-0.0068 Å °0.0166 Å °0.0237 Å °-0.021 Å °-0.0177 Å °
Refinement TLS groupSelection: ALL

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