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- PDB-5fcd: Crystal structure of MccD protein -

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Basic information

Entry
Database: PDB / ID: 5fcd
TitleCrystal structure of MccD protein
Components
  • MccD
  • UNK-UNK-UNK-MSE-UNK
  • UNK-UNK-UNK-UNK-MSE-UNK
KeywordsTRANSFERASE / MccD protein / methyltransferase fold / SAM binding / McC binding / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyS-adenosyl-L-methionine-dependent methyltransferase / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / MccD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsNocek, B. / Jedrzejczak, R. / Anderson, W.F. / Severinov, K. / Dubiley, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of MccD protein.
Authors: Nocek, B. / Jedrzejczak, R. / Anderson, W.F. / Severinov, K. / Dubiley, S. / Joachimiak, A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: UNK-UNK-UNK-MSE-UNK
E: UNK-UNK-UNK-UNK-MSE-UNK
A: MccD
B: MccD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3995
Polymers64,3644
Non-polymers351
Water4,774265
1
D: UNK-UNK-UNK-MSE-UNK
A: MccD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1753
Polymers32,1392
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: UNK-UNK-UNK-UNK-MSE-UNK
B: MccD


Theoretical massNumber of molelcules
Total (without water)32,2242
Polymers32,2242
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: UNK-UNK-UNK-MSE-UNK
E: UNK-UNK-UNK-UNK-MSE-UNK
A: MccD
B: MccD
hetero molecules

D: UNK-UNK-UNK-MSE-UNK
E: UNK-UNK-UNK-UNK-MSE-UNK
A: MccD
B: MccD
hetero molecules

D: UNK-UNK-UNK-MSE-UNK
E: UNK-UNK-UNK-UNK-MSE-UNK
A: MccD
B: MccD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,19715
Polymers193,09112
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9760 Å2
ΔGint-111 kcal/mol
Surface area65350 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)95.100, 95.100, 128.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein/peptide UNK-UNK-UNK-MSE-UNK


Mass: 536.525 Da / Num. of mol.: 1 / Details: The N-terminal part of MccD protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein/peptide UNK-UNK-UNK-UNK-MSE-UNK


Mass: 621.630 Da / Num. of mol.: 1 / Details: The N-terminal part of MccD protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Protein/peptide MccD / MccD protein


Mass: 31602.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccD
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q83Y56
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.6 M Na Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→39.22 Å / Num. obs: 38222 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19
Reflection shellResolution: 2.1→2.14 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→39.22 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.86 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 3270 4.98 %
Rwork0.1993 --
Obs0.2004 65623 94.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3690 0 1 265 3956
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0033794
f_angle_d0.7025138
f_dihedral_angle_d13.2831347
f_chiral_restr0.027552
f_plane_restr0.002668
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1005-2.13180.3004600.2619119637
2.1318-2.16510.3104830.2532162052
2.1651-2.20060.27181010.2469188461
2.2006-2.23860.27271140.2475213568
2.2386-2.27930.271200.2382244977
2.2793-2.32310.29641580.2622266685
2.3231-2.37050.25651220.2551291392
2.3705-2.4220.30111300.2503296093
2.422-2.47840.26161320.2408291094
2.4784-2.54040.27441590.2284297694
2.5404-2.6090.22321710.2193293994
2.609-2.68580.18591560.2156294294
2.6858-2.77240.2591760.2103294395
2.7724-2.87150.23831550.2029297895
2.8715-2.98640.2121740.2071297395
2.9864-3.12230.21821320.195296595
3.1223-3.28680.24231430.188302795
3.2868-3.49270.18451430.177299895
3.4927-3.76210.17131680.1537294995
3.7621-4.14030.18691750.1531297895
4.1403-4.73860.17191720.1508297395
4.7386-5.96670.21951440.1966301195
5.9667-39.22710.25741820.2321296895
Refinement TLS params.

Method: refined / Refinement-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)
10.0468-0.1030.00590.2321-0.01380.00070.01950.04630.0045-0.42410.408-1.02360.20610.9695-0.4480.609-0.03610.04030.93620.02671.2635.8070.81437.3697
28.05920.05831.12610.0107-0.11032.74490.09660.4426-0.0664-0.0912-0.06170.20720.144-0.1093-0.05251.2102-0.01440.23190.96830.25210.90118.8445-25.0322-37.0506
32.21911.89510.45874.6396-0.32273.9003-0.0891-0.0767-0.13650.08050.049-0.4033-0.04510.25840.0150.15850.0318-0.00710.2652-0.00010.206222.5173-5.22088.1708
42.2613-0.16510.09992.7304-0.06033.3009-0.0549-0.0277-0.28420.00020.0313-0.30380.28150.1995-0.0060.21160.06890.01410.25050.02660.231321.5271-17.59858.8116
51.88441.10730.38132.8607-0.39273.9714-0.02420.2669-0.166-0.23050.1253-0.18950.29440.1844-0.11580.18550.07490.0080.27160.00160.188216.0979-9.0845-5.2386
64.34270.4318-0.24661.8798-0.86322.70820.15680.73430.2519-0.3038-0.125-0.3565-0.02240.4367-0.05330.26590.06210.05590.37720.06420.268229.13591.0637-8.6645
75.8707-2.14210.00881.44310.24470.1788-0.0130.19150.36180.0190.023-0.7221-0.10730.2439-0.05620.2884-0.021-0.00580.36130.03530.596638.2173-0.51381.125
83.4857-3.49381.18513.8316-0.65211.83530.33640.9013-0.3924-0.09580.1152-0.48540.08860.1243-0.47570.2919-0.00830.04110.6666-0.07240.965148.5915-6.6141-4.9612
95.09082.05970.83392.9094-0.29292.73390.02720.03010.4932-0.1937-0.2537-0.1628-0.26550.13390.19630.28840.05610.03440.15830.03190.253621.0423.8018-0.9011
101.86140.3820.04532.2647-0.1692.3568-0.0034-0.1077-0.08310.0029-0.0088-0.22030.11090.30340.03110.11940.05250.00030.25680.03810.162122.2896-7.3551-34.1233
115.16510.92680.65261.8569-0.29384.00440.24840.5750.2002-0.1842-0.3598-0.4745-0.26331.32380.33850.65240.3543-0.1171.5470.63390.552523.2141-29.9316-15.7829
121.39512.80070.81076.687-1.20757.823-0.1572-0.3845-0.38650.82080.6178-0.18990.7918-0.0257-0.31980.3580.08380.00040.41030.08920.298112.5583-16.6478-20.297
132.1852-1.56450.64931.4456-0.49150.25550.1888-0.2224-0.57890.07510.0975-0.62370.4002-0.0679-0.2720.43070.0383-0.08970.24630.04060.858220.0393-26.9046-33.028
141.2066-0.7051-0.00241.53530.4761.22480.229-0.1365-0.42380.50370.302-1.14030.2586-0.1336-0.24040.72510.1518-0.47050.14690.20621.162927.23-34.3638-26.3551
152.06021.5524-0.57287.22230.68444.12570.0246-0.05450.0116-0.00330.0010.52280.2524-0.3914-0.04640.127-0.0102-0.0310.26980.04690.19419.9799-11.7114-30.8924
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11chain 'D' and (resid -1 through 3 )
22chain 'E' and (resid -3 through 2 )
33chain 'A' and (resid 29 through 62 )
44chain 'A' and (resid 63 through 106 )
55chain 'A' and (resid 107 through 144 )
66chain 'A' and (resid 145 through 191 )
77chain 'A' and (resid 192 through 224 )
88chain 'A' and (resid 236 through 256 )
99chain 'A' and (resid 257 through 267 )
1010chain 'B' and (resid 30 through 163 )
1111chain 'B' and (resid 164 through 174 )
1212chain 'B' and (resid 175 through 192 )
1313chain 'B' and (resid 193 through 225 )
1414chain 'B' and (resid 236 through 256 )
1515chain 'B' and (resid 257 through 267 )

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