[English] 日本語
Yorodumi
- PDB-4dip: Crystal structure of human Peptidyl-prolyl cis-trans isomerase FKBP14 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dip
TitleCrystal structure of human Peptidyl-prolyl cis-trans isomerase FKBP14
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP14
KeywordsISOMERASE / Structural Genomics / Structural Genomics Consortium / SGC / Peptidyl-prolyl cis-trans isomerase
Function / homology
Function and homology information


XBP1(S) activates chaperone genes / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / endoplasmic reticulum lumen / calcium ion binding
Similarity search - Function
Endoplasmic reticulum targeting sequence. / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Endoplasmic reticulum targeting sequence. / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Peptidyl-prolyl cis-trans isomerase FKBP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsKrojer, T. / Kiyani, W. / Goubin, S. / Muniz, J.R.C. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Oppermann, U. ...Krojer, T. / Kiyani, W. / Goubin, S. / Muniz, J.R.C. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Oppermann, U. / Zschocke, J. / Yue, W.W. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human Peptidyl-prolyl cis-trans isomerase FKBP14
Authors: Krojer, T. / Kiyani, W. / Goubin, S. / Muniz, J.R.C. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Oppermann, U. / Zschocke, J. / Yue, W.W. / ...Authors: Krojer, T. / Kiyani, W. / Goubin, S. / Muniz, J.R.C. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Oppermann, U. / Zschocke, J. / Yue, W.W. / Structural Genomics Consortium (SGC)
History
DepositionJan 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP14
B: Peptidyl-prolyl cis-trans isomerase FKBP14
C: Peptidyl-prolyl cis-trans isomerase FKBP14
D: Peptidyl-prolyl cis-trans isomerase FKBP14
E: Peptidyl-prolyl cis-trans isomerase FKBP14
F: Peptidyl-prolyl cis-trans isomerase FKBP14
G: Peptidyl-prolyl cis-trans isomerase FKBP14
H: Peptidyl-prolyl cis-trans isomerase FKBP14
I: Peptidyl-prolyl cis-trans isomerase FKBP14
J: Peptidyl-prolyl cis-trans isomerase FKBP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,44212
Polymers140,32410
Non-polymers1182
Water15,367853
1
A: Peptidyl-prolyl cis-trans isomerase FKBP14


Theoretical massNumber of molelcules
Total (without water)14,0321
Polymers14,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase FKBP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0552
Polymers14,0321
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidyl-prolyl cis-trans isomerase FKBP14


Theoretical massNumber of molelcules
Total (without water)14,0321
Polymers14,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptidyl-prolyl cis-trans isomerase FKBP14


Theoretical massNumber of molelcules
Total (without water)14,0321
Polymers14,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Peptidyl-prolyl cis-trans isomerase FKBP14


Theoretical massNumber of molelcules
Total (without water)14,0321
Polymers14,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Peptidyl-prolyl cis-trans isomerase FKBP14


Theoretical massNumber of molelcules
Total (without water)14,0321
Polymers14,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Peptidyl-prolyl cis-trans isomerase FKBP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1272
Polymers14,0321
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Peptidyl-prolyl cis-trans isomerase FKBP14


Theoretical massNumber of molelcules
Total (without water)14,0321
Polymers14,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Peptidyl-prolyl cis-trans isomerase FKBP14


Theoretical massNumber of molelcules
Total (without water)14,0321
Polymers14,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Peptidyl-prolyl cis-trans isomerase FKBP14


Theoretical massNumber of molelcules
Total (without water)14,0321
Polymers14,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.120, 64.060, 80.810
Angle α, β, γ (deg.)81.23, 75.21, 73.38
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Peptidyl-prolyl cis-trans isomerase FKBP14 / PPIase FKBP14 / 22 kDa FK506-binding protein / 22 kDa FKBP / FKBP-22 / FK506-binding protein 14 / ...PPIase FKBP14 / 22 kDa FK506-binding protein / 22 kDa FKBP / FKBP-22 / FK506-binding protein 14 / FKBP-14 / Rotamase


Mass: 14032.390 Da / Num. of mol.: 10 / Fragment: unp residues 19-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP14, FKBP22, UNQ322/PRO381 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NWM8, peptidylprolyl isomerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 853 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 277 K / pH: 7.2
Details: 18% PEG_3350, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.82→58.95 Å / Num. obs: 101237 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.099 / Net I/σ(I): 8
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.481 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→58.95 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.038 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.165 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5064 5 %RANDOM
Rwork0.203 ---
obs0.205 96170 96.6 %-
all-96170 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.26 Å2-0.14 Å2
2---0.03 Å2-0.37 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.82→58.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9328 0 6 853 10187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199716
X-RAY DIFFRACTIONr_bond_other_d0.010.026877
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9913151
X-RAY DIFFRACTIONr_angle_other_deg1.7983.00216936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04751236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70224.83383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.305151775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.9771529
X-RAY DIFFRACTIONr_chiral_restr0.0960.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110613
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021785
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 397 -
Rwork0.252 7014 -
obs--96.01 %
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)
111.13511.51026.20860.40071.53796.11390.02350.08560.21510.0122-0.07810.045-0.0246-0.15380.05460.0944-0.032-0.01850.0847-0.03880.1585-36.95228.121-56.635
21.37682.57950.87556.33841.69890.56-0.22080.10030.2027-0.36810.11560.253-0.13290.06610.10520.1148-0.0898-0.04880.1034-0.01330.1268-14.94842.368-51.474
33.39351.877-1.05961.62960.28062.91030.0479-0.2641-0.1429-0.01-0.1128-0.17450.1010.19590.06480.0478-0.0028-0.00550.0842-0.01190.0986-18.01424.361-47.347
48.3715-1.45123.1657.0558-1.69151.64310.3679-0.0559-1.2148-0.05660.2508-0.10040.11610.3045-0.61870.0298-0.0314-0.01630.577-0.23860.396-9.21723.158-48.282
51.3761.0259-0.09622.17990.22630.7912-0.08830.04580.0164-0.19140.03930.0149-0.04710.07930.0490.0555-0.0231-0.0240.1045-0.01570.0716-20.04525.772-53.49
632.00675.93925.65311.63950.01773.892-0.25610.2022-1.28170.08570.1953-0.19660.10870.18550.06080.0241-0.00250.02320.2029-0.06860.1254-37.24143.747-15.442
70.07810.60680.08784.95410.74410.12540.0182-0.01460.08590.0083-0.09550.5374-0.0352-0.0410.07730.12970.00010.03030.2058-0.02850.1746-14.19255.915-4.529
81.49640.0403-0.0851.7408-0.54561.0619-0.0020.0551-0.2362-0.0923-0.0532-0.09380.2131-0.03160.05520.065-0.024-0.02150.0855-0.02680.1101-10.440.3-3.673
91.15612.08320.88794.96960.79352.60080.13970.07630.0203-0.00640.06180.21640.2493-0.0687-0.20150.08860.0025-0.05820.1273-0.01750.1328-18.3242.421-7.732
100.77231.52640.24424.4899-1.4082.92220.0738-0.0670.0589-0.1771-0.04080.14960.3453-0.0468-0.03290.104-0.0159-0.01540.0762-0.01530.0834-13.44442.868-5.852
1133.12259.369814.9366.15512.8237.30531.5723-0.8108-0.6980.8536-1.03330.14370.5967-0.0311-0.5390.2904-0.0213-0.18530.3809-0.2180.394743.11231.789-13.987
123.04770.4297-1.93170.4702-0.68012.31430.2484-0.39760.23270.1756-0.07160.0578-0.14060.0847-0.17690.1251-0.0666-0.00270.1874-0.03070.126219.37224.436-15.064
133.23932.269-1.65865.1262-2.32332.3503-0.06350.25560.098-0.12660.0292-0.0168-0.0493-0.17760.03430.0586-0.0254-0.0430.09560.00530.062427.49827.563-32.153
141.40950.2489-0.90521.3842-0.08521.236-0.0439-0.0825-0.172-0.05070.024-0.03060.1072-0.0540.01990.0575-0.0297-0.03060.07-0.00110.084927.33919.974-23.852
153.19930.8443-1.03840.9103-0.68751.3275-0.0656-0.0548-0.0283-0.05550.0293-0.02340.0873-0.00480.03630.0557-0.0159-0.02260.0694-0.00940.063232.225.687-26.478
164.74110.92622.97510.79760.83172.18730.2102-0.06720.00980.1473-0.0633-0.0270.078-0.0927-0.14690.088-0.00360.04680.116-0.02670.125611.1615.23310.171
170.48990.54290.47041.34390.49012.00490.00180.13310.0044-0.0554-0.00120.0091-0.15950.1955-0.00060.0557-0.0296-0.01940.10680.02840.100225.98313.7045.257
187.57350.6117-2.35690.372-0.39291.7665-0.1907-0.3188-0.17840.09060.0287-0.12770.07010.05120.1620.079-0.0209-0.03510.09830.02250.107819.739-0.89917.2
191.88740.99920.061.3774-0.45510.43380.02510.11050.0410.029-0.02680.0119-0.0344-0.06980.00170.0579-0.0087-0.01460.1329-0.00050.08317.3077.8476.316
202.24721.568-0.51562.1604-0.61.25290.05190.03220.0110.0442-0.0306-0.03980.0264-0.0193-0.02130.03910.0136-0.0210.0647-0.00460.056718.0453.2898.852
219.63843.36175.34461.41862.19674.87880.0834-0.02880.10690.0851-0.0814-0.01630.1689-0.0243-0.0020.0639-0.0079-0.02580.04760.00050.142-16.90822.156-24.859
2213.087211.80780.538815.67280.93460.0626-0.11250.48950.1583-0.23810.0770.3043-0.0183-0.0160.03550.0954-0.0531-0.03420.1416-0.08370.17331.24236.382-15.894
231.23580.10240.07540.715-0.14271.4163-0.07760.0053-0.1782-0.0045-0.0229-0.0957-0.0180.09390.10050.0367-0.0249-0.01240.0952-0.01310.07752.37517.791-20.365
240.85741.2068-0.412.59260.26861.3706-0.05440.08910.05090.02320.06210.13870.0650.0684-0.00770.0537-0.0148-0.03170.1104-0.02880.1047-6.00116.39-23.797
252.47841.9684-0.30662.8448-0.74451.60810.0046-0.0332-0.1403-0.0813-0.0984-0.0591-0.0160.15630.09380.0423-0.00490.00060.0811-0.01120.07990.53920.505-22.223
2611.54110.45823.18250.7226-0.30311.29610.01880.08950.14910.0804-0.08120.03260.06580.02370.06240.0924-0.03180.00710.1163-0.05520.079622.89257.441-0.548
272.45730.6148-0.69991.15880.08050.56280.0162-0.2032-0.08760.06710.02640.03870.1416-0.0465-0.04250.077-0.0272-0.02610.156-0.00240.10427.33345.341-2.693
284.2812.4096-2.566910.0623-0.562.5692-0.03620.04160.2484-0.2593-0.07720.0511-0.043-0.24150.11340.0975-0.0297-0.02210.1082-0.03510.100218.35758.015-18.354
290.59020.9444-0.45643.14930.43051.8641-0.15610.1178-0.2044-0.38340.2783-0.21130.01170.0499-0.12230.0899-0.05810.02680.1516-0.05720.268513.04443.514-14.672
301.14050.2937-0.40051.0258-0.48781.2570.0542-0.0907-0.0591-0.0047-0.0093-0.0601-0.01030.1291-0.04480.0207-0.0083-0.01010.1211-0.04550.086218.86550.756-9.568
3112.8922.1194.74860.94180.18032.4023-0.0623-0.03370.3411-0.0349-0.07130.05230.07550.02840.13370.1136-0.02930.00160.0919-0.05040.1417-10.33121.18115.915
321.6674-0.2306-0.1251.2119-0.26990.339-0.0641-0.1977-0.12840.00690.0235-0.00810.0174-0.04220.04050.058-0.0209-0.00740.13990.00010.0663-23.0028.00412.827
334.27144.31490.967718.48440.93760.2227-0.19280.07920.5581-0.02480.06620.3485-0.05760.00560.12660.1205-0.0214-0.01980.1333-0.00160.1059-11.36723.797-1.122
341.15660.9755-0.0160.93390.22350.52610.019-0.0298-0.0760.0211-0.0077-0.0799-0.0140.0575-0.01130.0528-0.0057-0.00190.0941-0.00440.0811-14.10812.0825.47
352.02920.6956-0.18361.0516-0.19060.5440.02450.0402-0.01030.00020.0137-0.0286-0.00830.0794-0.03810.0677-0.0084-0.00730.0934-0.02890.0561-11.86813.024.118
3611.68953.94945.41521.79281.16783.69530.07780.05350.50910.1227-0.1170.20350.06370.05750.03920.1585-0.0728-0.03630.20660.00120.200318.6541.077-46.514
372.0241-0.386-0.17780.4522-0.07170.0555-0.1071-0.1522-0.1038-0.0060.11930.13850.0472-0.0457-0.01220.1302-0.05210.00730.2012-0.03680.11773.26628.904-48.26
387.28135.6046-0.01968.0783-0.89990.3628-0.02090.2290.1271-0.2173-0.01540.04870.0466-0.08920.03630.0865-0.0043-0.0230.135-0.00980.055213.62337.342-65.257
393.29590.2021-3.27614.2028-3.757115.8206-0.0750.2719-0.1911-0.6892-0.00080.15820.7712-0.29140.07590.1388-0.04680.00290.1008-0.06940.13966.05724.888-63.659
401.84710.0762-0.44450.96260.13290.3413-0.0169-0.0677-0.00960.10410.0081-0.01450.0801-0.00760.00880.068-0.0043-0.00450.1026-0.01640.077414.59431.895-54.204
4115.09893.76229.00962.95082.31818.02210.13610.16230.21720.3779-0.16080.12410.41540.04480.02470.16320.0131-0.0170.0649-0.00720.0815.6556.926-42.367
425.77872.3001-13.218.8132-1.258232.22630.0650.17070.1908-0.7480.2230.3568-0.4395-0.3431-0.2880.4179-0.2782-0.14290.2482-0.00560.391636.70171.326-35.506
431.5934-0.6335-1.19084.2086-1.13264.7079-0.12090.04340.1881-0.0251-0.1014-0.5023-0.44030.33040.22230.1193-0.0879-0.04850.12560.03460.142638.1958.646-42.139
4411.17942.3343-3.28551.00020.35323.3637-0.1569-0.3954-0.26570.0783-0.0979-0.05330.11170.07050.25480.13210.0211-0.06430.12270.03230.14532.94147.455-29.056
451.64830.3449-0.14731.8803-0.46651.7277-0.09080.08080.0468-0.0357-0.0061-0.1314-0.1540.04660.09690.0481-0.0142-0.03220.08580.00310.083430.54252.551-39.787
469.31533.51035.64933.10662.32123.46570.1716-0.75680.43340.2102-0.41110.46240.1374-0.42780.23950.0525-0.0189-0.01030.225-0.11470.2038-0.46566.221-32.437
473.2687-1.16451.86341.0579-0.22467.5578-0.1864-0.4387-0.05550.06610.00890.04330.5119-0.70540.17750.1205-0.0792-0.0350.25350.01220.1625-7.04352.225-35.539
485.24623.20330.682313.0754-1.89062.44110.25590.2547-0.1182-0.334-0.309-0.05920.1685-0.17180.05310.1235-0.0112-0.09040.11960.00150.10180.08164.267-51.302
492.05910.6106-0.5220.5714-0.23831.045-0.081-0.12610.047-0.14920.04170.10530.1409-0.06510.03920.0673-0.0238-0.05750.0861-0.00340.1079-0.07157.424-40.916
501.93791.02910.11131.6918-0.37492.3016-0.0225-0.13310.1095-0.35710.00860.19010.18090.06450.01390.1162-0.0103-0.06830.0570.00110.11643.10859.639-44.82
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 30
2X-RAY DIFFRACTION2A31 - 43
3X-RAY DIFFRACTION3A44 - 63
4X-RAY DIFFRACTION4A64 - 78
5X-RAY DIFFRACTION5A79 - 138
6X-RAY DIFFRACTION6B18 - 25
7X-RAY DIFFRACTION7B26 - 43
8X-RAY DIFFRACTION8B44 - 82
9X-RAY DIFFRACTION9B83 - 118
10X-RAY DIFFRACTION10B119 - 138
11X-RAY DIFFRACTION11C19 - 28
12X-RAY DIFFRACTION12C29 - 46
13X-RAY DIFFRACTION13C47 - 68
14X-RAY DIFFRACTION14C69 - 99
15X-RAY DIFFRACTION15C100 - 138
16X-RAY DIFFRACTION16D20 - 37
17X-RAY DIFFRACTION17D38 - 52
18X-RAY DIFFRACTION18D53 - 73
19X-RAY DIFFRACTION19D74 - 113
20X-RAY DIFFRACTION20D114 - 138
21X-RAY DIFFRACTION21E19 - 32
22X-RAY DIFFRACTION22E33 - 38
23X-RAY DIFFRACTION23E39 - 82
24X-RAY DIFFRACTION24E83 - 121
25X-RAY DIFFRACTION25E122 - 138
26X-RAY DIFFRACTION26F19 - 33
27X-RAY DIFFRACTION27F34 - 52
28X-RAY DIFFRACTION28F53 - 65
29X-RAY DIFFRACTION29F66 - 82
30X-RAY DIFFRACTION30F83 - 137
31X-RAY DIFFRACTION31G19 - 34
32X-RAY DIFFRACTION32G35 - 52
33X-RAY DIFFRACTION33G53 - 60
34X-RAY DIFFRACTION34G61 - 112
35X-RAY DIFFRACTION35G113 - 138
36X-RAY DIFFRACTION36H19 - 33
37X-RAY DIFFRACTION37H34 - 52
38X-RAY DIFFRACTION38H53 - 68
39X-RAY DIFFRACTION39H69 - 76
40X-RAY DIFFRACTION40H77 - 137
41X-RAY DIFFRACTION41I17 - 32
42X-RAY DIFFRACTION42I33 - 38
43X-RAY DIFFRACTION43I39 - 53
44X-RAY DIFFRACTION44I54 - 73
45X-RAY DIFFRACTION45I74 - 136
46X-RAY DIFFRACTION46J20 - 38
47X-RAY DIFFRACTION47J39 - 51
48X-RAY DIFFRACTION48J52 - 68
49X-RAY DIFFRACTION49J69 - 112
50X-RAY DIFFRACTION50J113 - 137

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more