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- PDB-3k13: Structure of the pterin-binding domain MeTr of 5-methyltetrahydro... -

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Basic information

Entry
Database: PDB / ID: 3k13
TitleStructure of the pterin-binding domain MeTr of 5-methyltetrahydrofolate-homocysteine methyltransferase from Bacteroides thetaiotaomicron
Components5-methyltetrahydrofolate-homocysteine methyltransferase
KeywordsTRANSFERASE / 5-methyltetrahydrofolate / methyltransferase / TIM barrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


pteridine-containing compound metabolic process / methionine synthase / methionine synthase activity / cobalamin binding / methylation / zinc ion binding / cytosol
Similarity search - Function
Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain ...Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Chem-THH / Methionine synthase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCuff, M.E. / Li, H. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the pterin-binding domain MeTr of 5-methyltetrahydrofolate-homocysteine methyltransferase from Bacteroides thetaiotaomicron
Authors: Cuff, M.E. / Li, H. / Cobb, G. / Joachimiak, A.
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-methyltetrahydrofolate-homocysteine methyltransferase
B: 5-methyltetrahydrofolate-homocysteine methyltransferase
C: 5-methyltetrahydrofolate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,45723
Polymers100,9653
Non-polymers2,49220
Water12,322684
1
A: 5-methyltetrahydrofolate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4928
Polymers33,6551
Non-polymers8377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 5-methyltetrahydrofolate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5298
Polymers33,6551
Non-polymers8747
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 5-methyltetrahydrofolate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4377
Polymers33,6551
Non-polymers7826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.652, 79.992, 127.068
Angle α, β, γ (deg.)90.000, 90.120, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein 5-methyltetrahydrofolate-homocysteine methyltransferase


Mass: 33654.863 Da / Num. of mol.: 3 / Fragment: sequence database residues 345-641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_0180 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21 / References: UniProt: Q8ABD0

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Non-polymers , 5 types, 704 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-THH / N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID / 5-METHYLTETRAHYDROFOLATE / Levomefolic acid


Mass: 459.456 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.09M Na HEPES pH 7.5, 1.26 Na citrate, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 ,0.97951
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979511
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 19.57 / Number: 433679 / Rmerge(I) obs: 0.109 / Χ2: 1.79 / D res high: 2 Å / D res low: 50 Å / Num. obs: 92713 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.435098.510.0935.7774.6
4.315.4310010.0793.774.6
3.764.3110010.0863.6114.6
3.423.7610010.0993.3374.7
3.173.4210010.1042.7924.7
2.993.1710010.1142.2384.7
2.842.9910010.1251.9524.7
2.712.8410010.1391.6824.7
2.612.7110010.1541.3524.7
2.522.6110010.1691.2544.7
2.442.5210010.1841.1364.7
2.372.4410010.1991.0284.7
2.312.3710010.2180.9724.7
2.252.3110010.2490.8654.7
2.22.2510010.2630.8074.7
2.152.210010.3020.7454.7
2.112.1510010.3450.7054.7
2.072.1110010.410.6374.7
2.032.0710010.470.6194.7
22.0310010.5310.5954.7
ReflectionResolution: 2→50 Å / Num. all: 92713 / Num. obs: 92713 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.109 / Χ2: 1.792 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.531 / Num. unique all: 4593 / Χ2: 0.595 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.377 / FOM acentric: 0.382 / FOM centric: 0.249 / Reflection: 92695 / Reflection acentric: 89295 / Reflection centric: 3400
Phasing MAD set

Highest resolution: 2 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.4110.40.400892953400
20.890.8514.522.50.820.62773033095
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
112.5-501.52121.10030877
17.14-12.51.1611.81.4001512171
15-7.141.3211.30.9003688280
13.85-51.0511.10.9006822377
13.12-3.851.1610.70.60010923480
12.63-3.121.610.40.20015912581
12.27-2.632.1210.30.10021813676
12-2.273.1810.100028317758
212.5-500.710.6826.623.91.661.3530777
27.14-12.50.730.7224.428.51.51.091510171
25-7.140.690.6918.223.91.721.233686280
23.85-50.820.820.226.91.160.796817377
23.12-3.850.870.8417.925.10.920.6210921480
22.63-3.120.910.8913.419.80.820.5315909581
22.27-2.630.970.9912.219.90.560.2921792676
22-2.2711.0111.919.80.380.1916361453
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se33.41588-0.928-0.201-0.4760
2Se35.72654-1.011-0.473-0.1460
3Se34.64759-0.734-0.135-0.4740
4Se31.42091-0.986-0.583-0.1050
5Se34.49593-1.08-0.265-0.1870
6Se37.93533-0.963-0.732-0.0880
7Se35.12867-0.985-0.63-0.0560
8Se40.06611-1.096-0.277-0.1430
9Se33.91522-0.828-0.299-0.5470
10Se30.5891-0.926-0.593-0.1190
11Se37.70253-1.145-0.148-0.2780
12Se36.27307-1.123-0.173-0.2290
13Se33.06654-0.93-0.232-0.5210
14Se45.16746-0.98-0.175-0.5810
15Se37.05326-0.839-0.193-0.6110
16Se44.48857-1.226-0.018-0.1410
17Se36.16846-1.098-0.079-0.2140
18Se44.84163-0.961-0.816-0.1910
19Se34.8021-0.777-0.174-0.5790
20Se45.11645-1.185-0.063-0.2450
21Se61.7084-1.069-0.452-0.0830
22Se43.05812-1.025-0.491-0.190
23Se40.73581-0.863-0.213-0.5620
24Se48.63437-0.742-0.4-0.6430
25Se155.98828-1.1-0.361-0.2510
26Se349.888-0.592-0.043-0.5140
27Se30.94011-0.928-0.202-0.476-0.178
28Se33.35274-1.011-0.473-0.146-0.167
29Se32.50113-0.733-0.134-0.474-0.158
30Se26.23591-0.986-0.583-0.105-0.132
31Se30.86985-1.08-0.265-0.187-0.148
32Se33.85485-0.963-0.732-0.088-0.101
33Se35.52032-0.985-0.63-0.056-0.147
34Se38.46782-1.096-0.277-0.143-0.132
35Se32.18943-0.828-0.299-0.547-0.109
36Se32.62672-0.926-0.592-0.119-0.153
37Se40.39467-1.145-0.147-0.278-0.124
38Se33.07479-1.123-0.173-0.228-0.102
39Se29.01975-0.93-0.232-0.521-0.082
40Se46.19651-0.98-0.175-0.581-0.083
41Se35.40531-0.84-0.193-0.61-0.075
42Se42.45826-1.226-0.019-0.141-0.077
43Se34.49064-1.098-0.078-0.213-0.079
44Se40.53364-0.96-0.817-0.192-0.056
45Se29.31851-0.777-0.176-0.579-0.058
46Se41.30637-1.185-0.062-0.245-0.053
47Se62.78091-1.068-0.451-0.083-0.096
48Se33.14703-1.025-0.492-0.191-0.05
49Se38.40618-0.863-0.213-0.562-0.024
50Se100.02-0.742-0.402-0.642-0.05
51Se167.28235-1.1-0.361-0.25-0.049
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.6760.730.46338530877
7.14-12.50.6930.7160.48816831512171
5-7.140.7460.7620.53539683688280
3.85-50.6380.6490.44271996822377
3.12-3.850.5880.5980.3541140310923480
2.63-3.120.4930.5020.2491649315912581
2.27-2.630.3150.3220.1072248921813676
2-2.270.1410.1430.0332907528317758
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 92695
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.84-10055.90.67603
7.67-10.8439.70.9271069
6.26-7.6737.50.9361405
5.42-6.26360.9431691
4.85-5.4237.90.9441875
4.43-4.8542.10.9432074
4.1-4.4344.50.9392274
3.83-4.146.20.9272392
3.61-3.8346.30.9272579
3.43-3.61480.9152748
3.27-3.4346.80.9082848
3.13-3.2750.20.9052979
3.01-3.1349.50.8993086
2.9-3.0149.20.8923250
2.8-2.950.50.8943350
2.71-2.854.10.8833445
2.63-2.7155.80.8773565
2.56-2.63570.8763663
2.49-2.56580.8743725
2.42-2.4960.10.8813870
2.37-2.42630.8774026
2.31-2.3762.20.8744026
2.26-2.3167.80.8634125
2.21-2.2667.80.8694245
2.17-2.2171.40.8794348
2.13-2.1772.70.8744424
2.09-2.1375.50.8654446
2.05-2.0979.40.8514597
2-2.0582.10.7915967

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2→46.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.165 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.92 / SU B: 5.719 / SU ML: 0.074 / SU R Cruickshank DPI: 0.12 / SU Rfree: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.113
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4638 5 %RANDOM
Rwork0.16 ---
all0.162 92703 --
obs0.162 92703 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.56 Å2 / Biso mean: 30.564 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0.45 Å2
2--0.28 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6682 0 166 684 7532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227164
X-RAY DIFFRACTIONr_bond_other_d0.0010.024867
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9789707
X-RAY DIFFRACTIONr_angle_other_deg0.8663.00211812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385909
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74324.444351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.625151255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1341557
X-RAY DIFFRACTIONr_chiral_restr0.0860.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021425
X-RAY DIFFRACTIONr_mcbond_it0.8561.54361
X-RAY DIFFRACTIONr_mcbond_other0.2111.51783
X-RAY DIFFRACTIONr_mcangle_it1.64627045
X-RAY DIFFRACTIONr_scbond_it2.60532803
X-RAY DIFFRACTIONr_scangle_it4.4034.52635
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 327 -
Rwork0.223 6053 -
all-6380 -
obs--92.99 %
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)
10.95870.1894-0.02531.4142-0.21070.7286-0.00790.0098-0.08050.07950.05130.0039-0.03330.0147-0.04330.0269-0.00280.01180.06450.00550.012764.068268.549716.1096
21.13860.3323-0.13641.1948-0.13860.77260.00410.08490.03730.00350.039-0.07240.0279-0.0196-0.04310.04350.01020.00060.03520.01430.013988.270430.841526.3134
31.56670.05430.12780.83850.04630.77060.0756-0.04040.060.0446-0.0279-0.06350.0016-0.0329-0.04760.03940.0116-0.0120.04110.00630.015293.003222.772258.5295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A350 - 636
2X-RAY DIFFRACTION1A1 - 647
3X-RAY DIFFRACTION1A4 - 759
4X-RAY DIFFRACTION2B350 - 636
5X-RAY DIFFRACTION2B1 - 647
6X-RAY DIFFRACTION2B3 - 758
7X-RAY DIFFRACTION3C350 - 637
8X-RAY DIFFRACTION3C1 - 646
9X-RAY DIFFRACTION3C2 - 767

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