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- PDB-3bzb: Crystal structure of uncharacterized protein CMQ451C from the pri... -

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Basic information

Entry
Database: PDB / ID: 3bzb
TitleCrystal structure of uncharacterized protein CMQ451C from the primitive red alga Cyanidioschyzon merolae
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / uncharacterized protein / red alga / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homologyLysine methyltransferase / Lysine methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å
AuthorsMcCoy, J.G. / Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein CMQ451C from the primitive red alga Cyanidioschyzon merolae.
Authors: McCoy, J.G. / Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N.
History
DepositionJan 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Remark 999SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT AT THE UNIPROT KNOWLEDGEBASE DATABASE ...SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)62,2532
Polymers62,2532
Non-polymers00
Water23413
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)31,1271
Polymers31,1271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)31,1271
Polymers31,1271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.783, 103.783, 105.385
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uncharacterized protein


Mass: 31126.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (eukaryote) / Strain: strain 10D / Gene: CMQ451C / Plasmid: PVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: D0VWS8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the Well solution (9% PEG 5000, 1.44 M Tetramethylammonium ...Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the Well solution (9% PEG 5000, 1.44 M Tetramethylammonium chloride, 0.10 M Triethanolamine pH 8.0 ). Cryoprotected with fomblin, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97927 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.79→46.554 Å / Num. obs: 16619 / % possible obs: 99.4 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.126 / Χ2: 0.936 / Net I/σ(I): 11.232
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.79-2.910.10.7051.48715651.00194.8
2.9-3.0213.90.57416400.90399.3
3.02-3.1517.90.47916400.833100
3.15-3.3220.90.38716380.818100
3.32-3.5321.60.24816580.852100
3.53-3.821.60.17216550.917100
3.8-4.1821.50.1216760.997100
4.18-4.7921.40.10116711.001100
4.79-6.0321.20.09116891.013100
6.03-46.55420.10.05317871.02899.9

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 4 Å / Lowest resolution: 45.46 Å / Power centric: 0 / Reflection acentric: 4901

IDR cullis acentricPower acentricReflection centric
ISO_100911
ANO_10.7741.2860
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_115.96-45.46006051
ISO_111.65-15.960010545
ISO_19.61-11.650014752
ISO_18.37-9.610017452
ISO_17.52-8.370019447
ISO_16.88-7.520022455
ISO_16.38-6.880024347
ISO_15.97-6.380026153
ISO_15.64-5.970028247
ISO_15.35-5.640030347
ISO_15.1-5.350030855
ISO_14.89-5.10033356
ISO_14.7-4.890034749
ISO_14.53-4.70035546
ISO_14.38-4.530037258
ISO_14.24-4.380039449
ISO_14.12-4.240040048
ISO_14-4.120039954
ANO_115.96-45.460.4872.666600
ANO_111.65-15.960.5782.4621050
ANO_19.61-11.650.6632.1041470
ANO_18.37-9.610.6351.9971740
ANO_17.52-8.370.5982.1211940
ANO_16.88-7.520.5742.1592240
ANO_16.38-6.880.6311.8782430
ANO_15.97-6.380.5951.8172610
ANO_15.64-5.970.7181.3762820
ANO_15.35-5.640.7821.2253030
ANO_15.1-5.350.7871.1113080
ANO_14.89-5.10.8370.973330
ANO_14.7-4.890.8790.8163470
ANO_14.53-4.70.9440.7163550
ANO_14.38-4.530.9290.6443720
ANO_14.24-4.380.9630.5133940
ANO_14.12-4.240.9640.4554000
ANO_14-4.120.9730.3663990
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
14.93885.8757.141SE129.622.27
214.37899.52510.45SE130.242.29
34.84257.7411.786SE140.511.42
410.18758.9942.011SE150.721.36
527.0274.52713.268SE192.151.14
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 5802
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.3-10072.10.523501
7.31-9.366.50.828509
6.35-7.3166.70.819509
5.75-6.3568.70.82503
5.32-5.7566.10.823505
5-5.32690.819501
4.74-5680.872510
4.53-4.7468.70.849510
4.35-4.5373.60.852504
4.2-4.3573.90.799501
4-4.279.70.682749

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.79→46.554 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.275 / WRfactor Rwork: 0.217 / SU B: 29.187 / SU ML: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.546 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 842 5.083 %RANDOM
Rwork0.209 ---
obs0.212 16565 98.901 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.398 Å2
Baniso -1Baniso -2Baniso -3
1-2.783 Å21.391 Å20 Å2
2--2.783 Å20 Å2
3----4.174 Å2
Refinement stepCycle: LAST / Resolution: 2.79→46.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 0 13 3027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223079
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9554196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71622.794136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.66815477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7791529
X-RAY DIFFRACTIONr_chiral_restr0.0810.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022333
X-RAY DIFFRACTIONr_nbd_refined0.2150.21337
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22027
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.23
X-RAY DIFFRACTIONr_mcbond_it0.3811.51972
X-RAY DIFFRACTIONr_mcangle_it0.71523110
X-RAY DIFFRACTIONr_scbond_it1.01331240
X-RAY DIFFRACTIONr_scangle_it1.7514.51086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.8630.317550.3571032122288.953
2.863-2.9410.418690.3331092118997.645
2.941-3.0260.355760.281069115099.565
3.026-3.1190.218490.2471060111499.551
3.119-3.2210.253570.2381049110999.729
3.221-3.3340.308580.218984104399.904
3.334-3.460.235500.207978103099.806
3.46-3.6010.21490.194939988100
3.601-3.7610.225550.192878933100
3.761-3.9440.231460.186850896100
3.944-4.1570.176430.19283788199.886
4.157-4.4090.221400.18760800100
4.409-4.7120.222460.143735781100
4.712-5.0890.216240.16696720100
5.089-5.5730.249270.207641668100
5.573-6.2270.386260.229583609100
6.227-7.1850.366340.238516550100
7.185-8.7860.266160.194449465100
8.786-12.3660.215110.177361372100
12.366-46.5540.355110.33721422998.253
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)
115.4664.0077-4.0336.3096.984613.2849-0.1896-0.7681.87111.5818-0.0472-0.0042-1.36131.04680.23690.0772-0.138-0.1008-0.0791-0.05570.778534.195767.8513-13.0905
215.5443-3.4775-4.251414.9473-2.0121.78240.35881.73082.12750.3532-0.2008-1.267-2.31050.9028-0.1580.1996-0.11660.11780.26290.40510.616431.887366.1336-25.8257
34.1669-3.1284-1.03933.65081.82116.38010.29030.45841.195-0.1862-0.436-0.2977-0.6455-0.26050.14560.07050.05520.05930.24930.20150.468723.372860.6505-20.7744
47.97023.993-3.86729.4742.9126.6775-0.3585-0.83171.09351.00250.6148-0.7765-0.53340.5337-0.25630.16040.108-0.02810.3397-0.04510.208723.58756.4163-9.183
55.80163.6747-0.21046.1397-5.21156.7723-0.05880.24680.04590.083-0.08110.757-0.15870.0910.13990.09680.16310.0370.37990.08120.193120.515451.4492-18.0095
617.5556-3.995-2.42327.4315-3.37152.9220.27760.78950.1199-0.08-0.1210.47060.0697-0.3656-0.15660.13190.15110.02760.3823-0.0090.114520.561851.1431-24.4947
76.45950.417-4.16446.3867-4.02184.89940.39430.8761-0.8823-0.3739-0.25690.34640.50380.2677-0.13740.08580.17670.00350.5864-0.1510.169328.075244.8384-28.0302
812.87224.32514.62747.97352.724611.72540.97511.95961.0144-0.7104-0.71520.0162-0.43920.0205-0.25990.06190.10090.23610.6240.36820.225528.66655.968-32.7346
97.6411-10.028-5.68318.62010.93112.03030.59942.12440.8835-0.0765-0.7285-0.44821.81310.57110.12910.03960.13450.03990.91370.01430.236435.981245.2429-34.3026
1015.85.775-0.937110.63715.83185.57810.13721.70641.4656-1.6215-0.2707-0.3528-1.21680.20090.13340.14910.11270.15470.81510.45080.332534.191156.0681-35.0637
118.4824-2.31031.17911.5224-3.1088.8594-0.0505-0.2661-0.6190.197-0.1914-0.34420.01170.75410.24190.1822-0.06740.02090.39070.00430.25632.256661.5194-25.4882
121.62720.7744-0.61721.20011.55344.33670.1101-0.22920.3556-0.1014-0.05460.2077-0.6949-0.1481-0.05550.3281-0.01720.01890.2456-0.02190.2453-7.109367.9815-23.7235
134.33562.2005-1.06984.4232-5.260313.4962-0.0446-0.33570.07480.21770.2639-0.2866-0.39710.0805-0.21930.0919-0.0206-0.03320.4369-0.15120.1369-5.992462.3916-12.0822
1415.49196.3127-2.08398.2517-0.69739.38810.3601-1.10390.53220.4912-0.1203-0.2043-0.62750.6753-0.23970.18790.0761-0.03310.4030.05650.0421-5.06563.6412-10.7746
156.12026.3128.17946.7336-2.088213.6834-0.6249-0.96290.28931.39271.11320.5674-1.6087-0.363-0.48840.34340.14490.22661.0723-0.23670.3365-17.806367.4473-6.2906
161.73552.40920.01336.1749-3.96466.8257-0.1175-0.3088-0.0983-0.03550.25510.5430.1744-0.6286-0.13750.0589-0.0066-0.00870.4846-0.0050.2125-18.759158.1437-19.2841
1711.63853.74231.42692.70672.406520.1711-0.184-0.2971.68740.58660.09170.7772-1.8627-1.16370.09230.07720.24680.09310.4155-0.05060.4377-23.827970.6761-17.6451
184.1972-2.9938-4.22724.50026.639811.3613-0.4577-0.0681-0.4512-0.28040.37190.3450.5318-0.37970.08590.2137-0.0742-0.05040.35680.10340.2668-18.391654.9664-30.7685
1916.46714.0527-10.93524.51980.326812.9043-0.09230.53550.1211-0.26590.30290.4317-0.4856-0.7223-0.21060.17880.0416-0.08820.38330.12960.1364-20.240661.0285-30.7806
2025.8048-5.6184-10.00593.13612.06424.27130.07040.15090.8932-0.56430.1540.4519-0.5828-0.5381-0.22440.210.0361-0.08280.3710.12480.2354-19.558663.1468-29.7774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA29 - 5029 - 50
2X-RAY DIFFRACTION2AA62 - 8062 - 80
3X-RAY DIFFRACTION3AA81 - 10981 - 109
4X-RAY DIFFRACTION4AA110 - 128110 - 128
5X-RAY DIFFRACTION5AA139 - 149139 - 149
6X-RAY DIFFRACTION6AA150 - 174150 - 174
7X-RAY DIFFRACTION7AA175 - 192175 - 192
8X-RAY DIFFRACTION8AA193 - 207193 - 207
9X-RAY DIFFRACTION9AA216 - 228216 - 228
10X-RAY DIFFRACTION10AA229 - 265229 - 265
11X-RAY DIFFRACTION11BB29 - 6729 - 67
12X-RAY DIFFRACTION12BB68 - 9768 - 97
13X-RAY DIFFRACTION13BB98 - 11998 - 119
14X-RAY DIFFRACTION14BB120 - 148120 - 148
15X-RAY DIFFRACTION15BB149 - 162149 - 162
16X-RAY DIFFRACTION16BB163 - 185163 - 185
17X-RAY DIFFRACTION17BB186 - 196186 - 196
18X-RAY DIFFRACTION18BB197 - 221197 - 221
19X-RAY DIFFRACTION19BB222 - 240222 - 240
20X-RAY DIFFRACTION20BB256 - 265256 - 265

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