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- PDB-3ttg: Crystal structure of putative aminomethyltransferase from Leptosp... -

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Basic information

Entry
Database: PDB / ID: 3ttg
TitleCrystal structure of putative aminomethyltransferase from Leptospirillum rubarum
ComponentsPutative aminomethyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyProbable tRNA modification gtpase trme; domain 1 / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesLeptospirillum rubarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMichalska, K. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of putative aminomethyltransferase from Leptospirillum rubarum
Authors: Michalska, K. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Joachimiak, A.
History
DepositionSep 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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: Putative aminomethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2465
Polymers40,1041
Non-polymers1424
Water3,153175
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.616, 115.616, 75.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Putative aminomethyltransferase


Mass: 40104.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospirillum rubarum (bacteria) / Gene: EAY58150, UBAL2_82410567 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Condon Plus (DE3)-RIPL / References: UniProt: A3EQP6
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 296 K / pH: 6.9
Details: 0.5 M K3PO4/0.5 M Na3PO4, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34441 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Biso Wilson estimate: 36.98 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 3 / % possible all: 94.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.179 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.124 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1393 4.05 %RANDOM
Rwork0.184 ---
obs0.185 34384 98 %-
all-34384 --
Displacement parametersBiso mean: 44.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.884 Å20 Å20 Å2
2--1.884 Å20 Å2
3----3.768 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2→36.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 4 175 2855
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0135401HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.179751HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1474SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes786HARMONIC5
X-RAY DIFFRACTIONt_it5401HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.08
X-RAY DIFFRACTIONt_other_torsion2.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion344SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5811SEMIHARMONIC4
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2079 113 4.12 %
Rwork0.1835 2629 -
all0.1845 2742 -
obs--98.03 %
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)
10.34880.68930.42532.35190.24131.03280.0662-0.06710.06210.30680.0242-0.17550.0649-0.0171-0.0905-0.1129-0.00790.0156-0.0433-0.0437-0.012646.3493-22.83745.1566
20.01390.0689-0.11030.511-0.36130.46490.0026-0.00130.01060.00930.0392-0.02760.02570.0281-0.04180.02470.07270.07670.09060.04850.053651.5251-38.8725-8.6258
31.11490.23770.29821.9035-0.20941.54230.051-0.1126-0.0740.121-0.0229-0.20190.201-0.0861-0.028-0.0703-0.01760.0073-0.0706-0.0164-0.072645.8782-33.28033.6791
40.93140.44250.10051.73020.44950.73220.0039-0.03090.0681-0.03560.0568-0.0886-0.0602-0.134-0.0606-0.0639-0.01410.0168-0.0694-0.0284-0.021445.129-21.5144-2.8199
53.8747-0.29070.35135.25160.40921.2859-0.00990.0640.3388-0.3391-0.11450.2509-0.1239-0.2210.1244-0.07870.0418-0.0166-0.1056-0.0033-0.010237.0229-4.0687-4.8309
61.4793-0.65071.14892.11990.03752.23190.03920.20270.4681-0.2299-0.1104-0.2705-0.25230.02520.0712-0.04510.00710.06-0.1044-0.00790.051243.4616-3.9329-2.6626
Refinement TLS groupSelection details: chain A

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