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- PDB-3gir: Crystal structure of glycine cleavage system aminomethyltransfera... -

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Basic information

Entry
Database: PDB / ID: 3gir
TitleCrystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae
ComponentsAminomethyltransferase
KeywordsTRANSFERASE / BARTONELLA HENSELAE / GLYCINE CLEAVAGE SYSTEM / AMINOMETHYLTRANSFERASE / Aminotransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


aminomethyltransferase / glycine catabolic process / aminomethyltransferase activity / transaminase activity
Similarity search - Function
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 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
Glycine cleavage system T protein / Glycine cleavage system T protein
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Aminomethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9132
Polymers42,8901
Non-polymers231
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.980, 72.670, 138.020
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


Mass: 42890.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: HUSTON-1 / Gene: gcvT, BH12840 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6G2E9, UniProt: A0A0H3M6H9*PLUS, aminomethyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: PROPLEX SCREEN, H4: 1.4M NA MALONATE, BAHEA.00657.A AT 44.8 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.6→69.01 Å / Num. all: 70368 / Num. obs: 70368 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 26.43 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 16.45
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: pdb entry 1wsr, modified with ccp4 program chainsaw

1wsr


Resolution: 1.6→69.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.401 / SU ML: 0.049 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3550 5 %RANDOM
Rwork0.175 ---
obs0.176 70311 95.3 %-
all-70311 --
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 mean: 17.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å2-0 Å2-0 Å2
2---0.2 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.6→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 1 531 3355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222899
X-RAY DIFFRACTIONr_bond_other_d0.0010.021989
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9723950
X-RAY DIFFRACTIONr_angle_other_deg1.0234844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.96523.307127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32515475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2381522
X-RAY DIFFRACTIONr_chiral_restr0.120.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02616
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2361.51824
X-RAY DIFFRACTIONr_mcbond_other0.3961.5749
X-RAY DIFFRACTIONr_mcangle_it2.13622913
X-RAY DIFFRACTIONr_scbond_it3.22831075
X-RAY DIFFRACTIONr_scangle_it5.4364.51025
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 300 -
Rwork0.216 5033 -
obs--98.94 %

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