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- PDB-3cgw: Crystal structure of 2-phospho-(S)-lactate transferase from Metha... -

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Basic information

Entry
Database: PDB / ID: 3cgw
TitleCrystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei. Northeast Structural Genomics Consortium target MaR46
ComponentsLPPG:FO 2-phospho-L-lactate transferase
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Magnesium
Function / homology
Function and homology information


2-phospho-L-lactate transferase / LPPG:FO 2-phospho-L-lactate transferase activity / F420-0 metabolic process / magnesium ion binding
Similarity search - Function
CofD-like domain / CofD-like domains / Phosphoenolpyruvate transferase/2-phospho-L-lactate transferase / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...CofD-like domain / CofD-like domains / Phosphoenolpyruvate transferase/2-phospho-L-lactate transferase / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-phospho-L-lactate transferase
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Vorobiev, S.M. / Ciao, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Vorobiev, S.M. / Ciao, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Molecular insights into the biosynthesis of the f420 coenzyme.
Authors: Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A. / Chen, Y. / Zhou, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Galinier, A. / White, R.H. / Tong, L.
History
DepositionMar 6, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionMar 18, 2008ID: 2FFE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LPPG:FO 2-phospho-L-lactate transferase


Theoretical massNumber of molelcules
Total (without water)34,8381
Polymers34,8381
Non-polymers00
Water00
1
A: LPPG:FO 2-phospho-L-lactate transferase

A: LPPG:FO 2-phospho-L-lactate transferase


Theoretical massNumber of molelcules
Total (without water)69,6772
Polymers69,6772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1980 Å2
ΔGint-13.7 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.640, 110.640, 75.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein LPPG:FO 2-phospho-L-lactate transferase


Mass: 34838.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Species: Methanosarcina mazei / Strain: Go1 / DSM 3647 / Goe1 / JCM 11883 / OCM 88 / Gene: cofD, MM_1874 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
References: UniProt: Q8PVT6, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups

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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: 3.34 Å3/Da / Density % sol: 63.13 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Reservoir solution: 16% PEG 3350 and 200 mM LiNO3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97933, 0.97947, 0.96771
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2005 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979331
20.979471
30.967711
ReflectionResolution: 3.1→28.45 Å / Num. all: 16408 / Num. obs: 16408 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 71.4 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.091 / Net I/σ(I): 17.88
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.26 / Num. unique all: 1570 / Rsym value: 0.383 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→19.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 249701.43 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1241 9.5 %RANDOM
Rwork0.239 ---
all0.24 16314 --
obs0.239 13019 79.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.89 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 99.6 Å2
Baniso -1Baniso -2Baniso -3
1--38.99 Å20 Å20 Å2
2---38.99 Å20 Å2
3---77.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.96 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 0 0 2344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.388 74 10.3 %
Rwork0.373 647 -
obs-647 43.8 %

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