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- PDB-3n08: Crystal Structure of a Putative PhosphatidylEthanolamine-Binding ... -

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Basic information

Entry
Database: PDB / ID: 3n08
TitleCrystal Structure of a Putative PhosphatidylEthanolamine-Binding Protein (PEBP) Homolog CT736 from Chlamydia trachomatis D/UW-3/CX
ComponentsPutative PhosphatidylEthanolamine-Binding Protein (PEBP)
KeywordsPhosphatidylEthanolamine-Binding Protein / eukarytic homolog Raf Kinase Inhibitor Protein (RKIP). CSGID / Structural Genomics / National Institute of Allergy and Infectious Diseases / National Institutes of Health / Department of Health and Human Services / Center for Structural Genomics of Infectious Diseases
Function / homologyYbhB/YbcL / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta / UPF0098 protein CT_736
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.25 Angstrom Crystal Structure of a Putative PhosphatidylEthanolamine-Binding Protein (PEBP) Homolog CT736 from Chlamydia trachomatis D/UW-3/CX
Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative PhosphatidylEthanolamine-Binding Protein (PEBP)
B: Putative PhosphatidylEthanolamine-Binding Protein (PEBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8489
Polymers33,5862
Non-polymers2627
Water10,539585
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative PhosphatidylEthanolamine-Binding Protein (PEBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9846
Polymers16,7931
Non-polymers1915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Putative PhosphatidylEthanolamine-Binding Protein (PEBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8643
Polymers16,7931
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.115, 37.847, 55.101
Angle α, β, γ (deg.)105.44, 96.50, 108.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative PhosphatidylEthanolamine-Binding Protein (PEBP)


Mass: 16792.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: D/UW-3/CX / Gene: CT_736, ybcL / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: O84741
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 298 K / pH: 7
Details: 20%PEG 3350,0.2M Ca Chloride , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 70466 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.75
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.42 / % possible all: 92.3

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_348)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FUX
Resolution: 1.25→26.19 Å / SU ML: 0.13 / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.173 3540 5.02 %
Rwork0.152 --
obs0.153 70448 94.8 %
all-70448 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.73 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0914 Å20.0032 Å20.127 Å2
2---0.0771 Å20.0141 Å2
3----0.0143 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 7 585 2937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012614
X-RAY DIFFRACTIONf_angle_d1.3733600
X-RAY DIFFRACTIONf_dihedral_angle_d12.679975
X-RAY DIFFRACTIONf_chiral_restr0.084391
X-RAY DIFFRACTIONf_plane_restr0.009485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2491-1.29370.27213260.23326492X-RAY DIFFRACTION92
1.2937-1.34550.21233710.20416534X-RAY DIFFRACTION92
1.3455-1.40670.20743340.18626569X-RAY DIFFRACTION93
1.4067-1.48090.19643260.16676650X-RAY DIFFRACTION94
1.4809-1.57370.20113730.15266682X-RAY DIFFRACTION95
1.5737-1.69520.17513700.14486688X-RAY DIFFRACTION95
1.6952-1.86570.16973460.14176776X-RAY DIFFRACTION96
1.8657-2.13560.1583900.1356766X-RAY DIFFRACTION97
2.1356-2.69020.15973480.14076934X-RAY DIFFRACTION98
2.6902-26.19160.15513560.14486817X-RAY DIFFRACTION97
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)
10.17580.113-0.03110.0711-0.02270.0489-0.0144-0.07430.05210.22820.03840.0082-0.1640.05730.00020.10440.0107-0.0120.0768-0.01010.08645.95348.40249.6548
20.03340.0340.02250.04190.00960.0295-0.04190.00780.18550.13380.0478-0.0259-0.1264-0.0697-00.09340.0169-0.00890.0778-0.01330.0766-4.486812.40236.4114
30.0270.0038-0.0070.03140.00880.0224-0.0059-0.02040.0724-0.1204-0.0364-0.0659-0.1094-0.0191-0.00190.0896-0.0047-0.01350.06740.00940.0835-4.53814.2786-5.4621
40.08980.0295-0.01840.01840.01490.0503-0.05850.20790.0259-0.0540.0345-0.0004-0.05590.03520.00230.07320.0005-0.00770.08630.00930.069-3.10910.2675-7.3821
50.02360.00930.00480.0448-0.01430.0064-0.0499-0.06380.12370.141-0.037-0.1206-0.09680.028-0.00010.0825-0.0009-0.00910.0916-0.00450.093610.23674.67819.0405
60.02570.00420.01360.0120.02820.06520.0147-0.2339-0.02140.1280.0953-0.05090.05740.03290.00210.09570.021-0.01990.10860.00240.093517.7784-5.327310.3218
70.018-0.00430.00570.0002-0.00470.00270.0884-0.0984-0.1166-0.0348-0.03870.06460.0749-0.0395-0.00490.06830.0036-00.0693-0.00170.08630.1466-2.24792.6989
80.03490.0092-0.03890.07340.00030.04740.01240.0888-0.2418-0.1073-0.0114-0.14870.0651-0.00120.00010.11080.0050.01710.098-0.01240.1518-15.556-5.7564-1.4098
90.17-0.1109-0.1050.2993-0.06030.13540.05490.05470.0313-0.0321-0.0399-0.0532-0.01670.0376-0.00330.06920.01150.00470.0787-0.00840.09146.70290.52-2.6368
100.02350.0011-0.02330.00720.00950.03860.04810.23070.2294-0.2057-0.04570.0428-0.0068-0.15210.00020.11420.0066-0.00230.1247-0.02150.113-2.7576-4.9301-9.9173
110.04670.0028-0.02020.0383-0.01070.00930.12240.20820.0124-0.0907-0.0545-0.01080.0105-0.03660.00010.07830.00150.00070.098-0.00010.0968-7.84044.1535-6.5714
120.00650.00280.00030.0119-0.01150.01250.0068-0.08440.04510.0076-0.052-0.04640.0822-0.14200.0650.0001-0.0070.1023-0.00330.1018-16.26276.49560.984
130.1842-0.0376-0.04350.1553-0.11550.11030.01140.0027-0.0543-0.02510.00080.0180.05950.01330.01340.07280.0068-0.00460.0599-0.00520.08574.6253-4.99183.8735
140.1467-0.06180.0670.0778-0.07090.08150.15930.3012-0.08980.0585-0.0903-0.03250.1501-0.0136-0.00010.10620.025-0.01860.1199-0.00430.10291.8416-12.9671-1.757
150.16620.0633-0.02910.0243-0.00420.10350.0217-0.0333-0.08820.0336-0.00260.0830.0773-0.0186-0.01260.09370.01-0.02180.06440.00120.08553.7974-5.02179.4952
160.017-0.0164-0.00050.03980.00330.0651-0.00060.040.0044-0.04240.03130.1547-0.1567-0.2255-0.00260.07670.0136-0.01580.09630.00630.0868-12.974110.7851-1.5263
170.09770.03930.02820.0576-0.03020.0435-0.0439-0.06310.0739-0.0629-0.03370.1046-0.1229-0.0495-00.0984-0.0033-0.00780.08260.00290.09742.8184-5.384718.9831
180.93270.074-0.00450.10010.12270.35190.11830.04170.3579-0.01560.0112-0.0961-0.21560.12030.02760.1036-0.0262-0.01190.11030.02340.059113.8401-1.833921.1693
190.0175-0.0099-0.01480.01170.01120.013-0.058-0.11820.17080.14060.028-0.1142-0.18730.1667-00.1487-0.0242-0.01410.1222-0.01730.086812.4127-1.460134.194
200.19660.1458-0.2650.1569-0.18470.3527-0.0082-0.04080.04960.0531-0.00960.0309-0.0810.04380.00010.0909-0.0016-0.0030.1125-0.00960.08625.2697-6.932428.9088
210.0044-0.00730.00630.0116-0.01410.0321-0.13740.4028-0.0225-0.24120.12730.24330.1575-0.1649-0.00010.1746-0.1104-0.06140.25650.04240.1217-10.5272-18.323915.622
220.03040.0023-0.07190.0002-0.00970.18490.07010.1028-0.09480.025-0.0298-0.03350.12470.093-0.00120.0781-0.00510.00150.10920.01450.075610.6519-16.561225.0684
230.03580.0002-0.01610.04630.03330.03030.0823-0.1592-0.17140.16-0.11680.1573-0.0325-0.02270.00010.1121-0.00180.00960.12760.01270.162724.0641-22.822228.4059
240.19160.1501-0.19820.2058-0.10770.22380.0173-0.0090.0811-0.0072-0.01360.01350.0675-0.09710.00160.0763-0.0050.00530.1120.00360.08791.5778-15.036628.0508
250.00580.0041-0.00840.0056-0.00880.01490.08360.1840.19840.01290.1224-0.1081-0.0458-0.1613-0.00010.11710.00090.01220.1798-0.0360.13991.2115-5.821333.363
260.09360.12130.0290.1780.06890.04610.0789-0.28620.11990.0587-0.07070.12420.0488-0.12570.00010.1118-0.00120.01040.14950.0040.1032.7352-18.072434.5822
270.01160.01590.01130.0454-0.0030.0201-0.0854-0.21490.05440.15580.00910.08780.2371-0.06240.00010.1240.00010.01440.13060.00970.0959.9683-17.466436.7403
280.3518-0.0481-0.25090.1107-0.1320.54290.0388-0.066-0.07790.0486-0.0366-0.03850.1730.044-0.10970.0949-0.0075-0.00580.10530.01570.07869.2764-16.398225.7724
290.03880.0016-0.03250.03180.02480.0544-0.1036-0.2626-0.0847-0.06360.09380.0632-0.0886-0.0147-0.00010.2127-0.0011-0.00280.1870.01410.12944.4376-26.750332.3173
300.01420.0069-0.00370.01850.00770.0066-0.12760.1772-0.10220.07130.03390.20680.28270.1296-0.00010.29760.0214-0.03240.1113-0.00540.1197.4112-29.165224.3824
310.17640.00640.06360.1373-0.09570.1261-0.06030.1439-0.0896-0.2250.1062-0.21540.16150.0752-0.01240.1358-0.0156-0.02050.063-0.01270.05822.6529-20.61417.1373
320.0316-0.0415-0.01090.093-0.00080.0657-0.03230.00280.13830.1492-0.08420.0494-0.08830.33360.0190.1034-0.0366-0.01940.14780.0190.071319.9001-4.286229.6363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -1:6)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 7:14)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 15:18)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 19:28)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 29:35)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 36:39)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 40:48)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 49:59)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 60:87)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 88:94)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 95:101)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 102:105)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 106:121)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 122:131)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 132:145)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 146:149)
17X-RAY DIFFRACTION17(CHAIN B AND RESID -2:8)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 9:13)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 14:17)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 18:35)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 36:39)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 40:50)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 51:59)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 60:74)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 75:78)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 79:90)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 91:96)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 97:121)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 122:126)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 127:131)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 132:143)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 144:150)

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