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- PDB-3hh1: The Structure of a Tetrapyrrole methylase family protein domain f... -

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Basic information

Entry
Database: PDB / ID: 3hh1
TitleThe Structure of a Tetrapyrrole methylase family protein domain from Chlorobium tepidum TLS
ComponentsTetrapyrrole methylase family protein
KeywordsTRANSFERASE / tetrapyrrole methylase / Chlorobium tepidum / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Methyltransferase
Function / homology
Function and homology information


16S rRNA (cytidine1402-2'-O)-methyltransferase / : / rRNA (cytosine-2'-O-)-methyltransferase activity / cytoplasm
Similarity search - Function
rRNA small subunit methyltransferase I / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase I
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsCuff, M.E. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The Structure of a Tetrapyrrole methylase family protein domain from Chlorobium tepidum TLS.
Authors: Cuff, M.E. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 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: Tetrapyrrole methylase family protein
B: Tetrapyrrole methylase family protein
C: Tetrapyrrole methylase family protein
D: Tetrapyrrole methylase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,44911
Polymers49,8114
Non-polymers6387
Water4,197233
1
A: Tetrapyrrole methylase family protein
B: Tetrapyrrole methylase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3527
Polymers24,9052
Non-polymers4465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-12 kcal/mol
Surface area11740 Å2
MethodPISA
2
C: Tetrapyrrole methylase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5492
Polymers12,4531
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Tetrapyrrole methylase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5492
Polymers12,4531
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.986, 47.569, 64.497
Angle α, β, γ (deg.)90.000, 91.000, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein
Tetrapyrrole methylase family protein


Mass: 12452.724 Da / Num. of mol.: 4 / Fragment: residues 7-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Strain: TLS / Gene: CT1646 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KBY6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.95 Å3/Da / Density % sol: 36.94 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Ammonium Sulfate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945, 0.97931
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979311
ReflectionRedundancy: 7.6 % / Av σ(I) over netI: 20.76 / Number: 270515 / Rmerge(I) obs: 0.09 / Χ2: 1.31 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 35606 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.885098.910.0822.4597.2
3.884.8810010.0631.4287.5
3.393.8810010.0721.577.5
3.083.3910010.0871.6067.6
2.863.0810010.0961.4547.6
2.692.8610010.0981.3167.7
2.552.6910010.1021.1977.7
2.442.5510010.1061.0257.7
2.352.4410010.1261.0937.7
2.272.3510010.1361.0287.7
2.22.2710010.1480.9527.7
2.132.210010.1530.8967.7
2.082.1310010.1940.9677.7
2.032.0810010.2551.0637.7
1.982.0310010.2861.0157.7
1.941.9810010.3661.2037.7
1.91.9410010.451.4567.7
1.861.910010.5541.3637.6
1.831.8610010.681.4997.5
1.81.8310010.8531.6677.3
ReflectionResolution: 1.8→50 Å / Num. all: 35606 / Num. obs: 35606 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.309 / Net I/σ(I): 20.761
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.853 / Num. unique all: 1796 / Χ2: 1.667 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.8 Å / D res low: 50 Å / FOM : 0.285 / FOM acentric: 0.287 / FOM centric: 0.238 / Reflection: 35490 / Reflection acentric: 33549 / Reflection centric: 1941
Phasing MAD set

Highest resolution: 1.8 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.2610.10.100335491941
20.940.910.416.20.530.46263441642
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
111.5-501.110.40.20010339
16.5-11.51.1110.40.20055593
14.53-6.51.1310.30.2001367161
13.47-4.531.0110.20.2002527220
12.82-3.471.210.10.1004076274
12.37-2.821.4710.10005964335
12.05-2.371.67100008249385
11.8-2.055.031000010708434
211.5-500.840.9322.526.61.441.127532
26.5-11.50.750.7418.119.61.471.2251685
24.53-6.50.870.8318.2221.050.791367160
23.47-4.530.930.931927.20.650.412527217
22.82-3.470.950.8713.118.10.550.384076274
22.37-2.820.960.938.411.90.460.35964335
22.05-2.370.980.977.410.60.260.178245385
21.8-2.050.990.997.210.60.160.13574154
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se24.13416-0.724-0.46-0.1270
2Se28.01863-0.853-0.961-0.2080
3Se28.72545-0.892-0.421-0.3010
4Se34.83353-1.139-0.963-0.1740
5Se29.55244-0.698-0.872-0.3880
6Se21.62797-1.164-0.404-0.2980
7Se36.22593-0.427-0.83-0.3850
8Se39.9866-0.466-0.382-0.070
9Se36.25943-0.725-0.457-0.128-0.401
10Se44.54406-0.855-0.958-0.209-0.331
11Se39.96629-0.891-0.419-0.302-0.314
12Se50.28936-1.139-0.962-0.175-0.259
13Se38.60245-0.697-0.871-0.386-0.273
14Se65.0288-1.166-0.401-0.299-0.307
15Se67.22723-0.424-0.827-0.389-0.3
16Se48.20995-0.467-0.381-0.073-0.207
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.5-500.4510.4740.39314210339
6.5-11.50.6060.6250.49264855593
4.53-6.50.6120.6310.44715281367161
3.47-4.530.4950.5080.33727472527220
2.82-3.470.4670.4740.35643504076274
2.37-2.820.380.3870.25962995964335
2.05-2.370.2230.2270.15686348249385
1.8-2.050.090.0930.0261114210708434
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 35490
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.54-10054.80.751512
5.96-7.5450.40.863506
5.09-5.9653.80.87624
4.51-5.0948.90.896703
4.1-4.5151.90.902770
3.78-4.152.30.867846
3.52-3.7855.20.839912
3.31-3.5252.30.847964
3.14-3.3156.50.841023
2.99-3.1457.10.8271075
2.86-2.9956.70.8331124
2.74-2.8656.10.8471172
2.64-2.7453.70.8381207
2.55-2.6456.80.8341272
2.46-2.5559.90.8321312
2.39-2.4660.10.8241339
2.32-2.39600.8261395
2.26-2.3264.60.8111420
2.2-2.2664.70.8121468
2.15-2.266.60.8271505
2.1-2.1568.80.7891537
2.05-2.168.80.7861578
2.01-2.0570.80.7981584
1.96-2.0176.10.8031640
1.93-1.9676.60.7991646
1.89-1.9378.70.7921725
1.85-1.8981.10.7451690
1.8-1.8582.60.6982941

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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: 1.85→37.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.2 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.884 / SU B: 6.359 / SU ML: 0.096 / SU R Cruickshank DPI: 0.157 / SU Rfree: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1648 5 %RANDOM
Rwork0.181 ---
all0.183 32800 --
obs0.183 32800 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.84 Å2 / Biso mean: 26.295 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20.1 Å2
2--0.5 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3249 0 34 233 3516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223375
X-RAY DIFFRACTIONr_bond_other_d0.0010.022195
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9764599
X-RAY DIFFRACTIONr_angle_other_deg0.91535363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4865441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.38722.985134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99515527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9761529
X-RAY DIFFRACTIONr_chiral_restr0.0880.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213776
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02657
X-RAY DIFFRACTIONr_mcbond_it1.0181.52199
X-RAY DIFFRACTIONr_mcbond_other0.2861.5896
X-RAY DIFFRACTIONr_mcangle_it1.88323533
X-RAY DIFFRACTIONr_scbond_it2.92231176
X-RAY DIFFRACTIONr_scangle_it4.9574.51066
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 123 -
Rwork0.208 2283 -
all-2406 -
obs--98.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.7276-0.36173.50948.5688-2.8014.10050.4110.6015-0.16490.0373-0.547-0.5005-0.18780.20530.13590.10940.0035-0.02050.13940.03030.096628.276240.018611.5245
27.6840.8136-1.12122.9189-0.89053.89820.0648-0.4132-0.4620.09950.0618-0.1973-0.08260.3004-0.12660.1001-0.0022-0.01010.0930.01630.12842.846738.578216.56
33.6501-0.0092-0.92312.6321-0.12090.90070.0118-0.4069-0.15280.4142-0.077-0.0973-0.03640.07550.06530.1320.0016-0.02090.12030.04350.088831.677642.090124.3644
44.58-0.79680.56813.7053-3.44359.7089-0.1049-0.0982-0.02040.0478-0.07580.1230.1934-0.16010.18060.09730.01290.00070.0546-0.00460.117220.541941.769318.4297
52.4569-0.2367-0.45734.01790.04110.0899-0.00540.1509-0.24720.1288-0.0437-0.05410.0231-0.01540.04910.12950.0233-0.01690.09140.00050.12225.471831.836414.9218
64.8482-1.01310.10510.95250.97261.36380.045-0.06020.25550.09940.0706-0.1790.11810.0788-0.11560.10570.0103-0.01470.05140.02460.144533.804312.944616.6455
74.9718-1.4953-1.31353.2034-0.10111.46420.26070.68160.3475-0.5075-0.2128-0.3891-0.1056-0.1635-0.04790.17560.03420.04130.13350.05430.103333.022913.69294.3241
84.0636-0.30710.71733.2545-0.77191.54650.0130.14090.1771-0.2314-0.0120.32220.01-0.1228-0.0010.11630.0235-0.01660.09220.01340.105525.872211.426.8852
91.9861-2.23272.13212.6947-3.30877.6519-0.03850.1002-0.0104-0.09310.04780.02510.189-0.7813-0.00930.2781-0.068-0.03720.2666-0.03860.131715.279411.720313.1255
102.84240.0246-0.89313.3993-0.66362.0934-0.0046-0.13780.22150.0592-0.0505-0.0277-0.11720.06230.05510.0824-0.0061-0.01610.0584-0.0230.077624.620819.871616.9269
1112.41774.1707-8.50338.3227-5.11877.8268-0.1875-0.35790.1077-0.0414-0.2159-0.58780.2896-0.21020.40340.1646-0.02920.01250.2448-0.02440.27651.16641.828546.7017
124.44490.18860.07231.2759-0.30730.45430.10050.4110.3844-0.0269-0.0629-0.0878-0.0454-0.0337-0.03750.0532-0.0027-0.00090.16240.07090.143710.587436.516441.3668
139.4703-2.12650.02013.2204-0.3432.39950.22581.40480.0576-0.3355-0.2136-0.03240.0623-0.1974-0.01220.0707-0.0109-0.00580.36260.04080.04415.695331.355835.3455
147.1109-0.3228-1.22872.2081-0.43213.891-0.00260.87310.4191-0.05290.03820.2456-0.0556-0.264-0.03560.04160.0009-0.00980.2020.13620.185-5.34338.941339.5294
157.38581.2505-2.79342.89250.0329.9050.34760.00740.3681-0.2464-0.12130.0689-0.44610.6088-0.22620.0999-0.03240.03540.13720.08430.2368-2.612547.642543.4289
164.88580.8423-0.09971.43780.08610.85070.041-0.102-0.11940.0133-0.0610.03250.0585-0.06740.020.03940.02380.00220.08050.00470.0851-8.01443.354112.2883
176.22191.67721.46681.0671-0.8292.8169-0.26010.53150.0522-0.07660.1473-0.0247-0.1130.07160.11280.15510.0507-0.01990.1301-0.03310.0968-6.862750.16293.0591
186.8444-0.1042-2.66562.72810.31510.12230.00510.04510.0895-0.1234-0.0216-0.1087-0.02220.29630.01650.09410.0147-0.02140.09770.01380.15018.594148.669511.9137
191.7954-0.8369-0.16742.91922.94124.75020.05410.2508-0.4155-0.2111-0.14320.08520.0647-0.03290.08910.17710.01440.00940.1753-0.03470.2585-0.250437.13773.5353
205.8096-0.59852.10266.7713.28559.5251-0.0746-0.4313-0.15860.0903-0.17520.24910.6079-0.71610.24980.06980.01070.00220.2026-0.00560.2314.487737.821614.1843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 11
2X-RAY DIFFRACTION2A12 - 24
3X-RAY DIFFRACTION3A25 - 60
4X-RAY DIFFRACTION4A61 - 83
5X-RAY DIFFRACTION5A84 - 112
6X-RAY DIFFRACTION6B7 - 32
7X-RAY DIFFRACTION7B33 - 46
8X-RAY DIFFRACTION8B47 - 60
9X-RAY DIFFRACTION9B61 - 75
10X-RAY DIFFRACTION10B76 - 113
11X-RAY DIFFRACTION11C7 - 10
12X-RAY DIFFRACTION12C11 - 37
13X-RAY DIFFRACTION13C38 - 60
14X-RAY DIFFRACTION14C61 - 90
15X-RAY DIFFRACTION15C100 - 112
16X-RAY DIFFRACTION16D6 - 34
17X-RAY DIFFRACTION17D35 - 58
18X-RAY DIFFRACTION18D62 - 78
19X-RAY DIFFRACTION19D79 - 95
20X-RAY DIFFRACTION20D96 - 112

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