[English] 日本語
Yorodumi
- PDB-4j25: Crystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P4H) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j25
TitleCrystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P4H)
ComponentsPutative uncharacterized protein
KeywordsOXIDOREDUCTASE / 2-oxoglutarate oxygenase / oxygen sensing / double-stranded beta helix / jellyroll fold / prolyl-4-hydroxylase
Function / homology
Function and homology information


L-ascorbic acid binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding
Similarity search - Function
Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Fe2OG dioxygenase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsScotti, J.S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Human oxygen sensing may have origins in prokaryotic elongation factor Tu prolyl-hydroxylation
Authors: Scotti, J.S. / Leung, I.K.H. / Ge, W. / Bentley, M.A. / Paps, J. / Kramer, H.B. / Lee, J. / Aik, W. / Choi, H. / Paulsen, S.M. / Bowman, L.A.H. / Loik, N.D. / Horita, S. / Ho, C.H. / ...Authors: Scotti, J.S. / Leung, I.K.H. / Ge, W. / Bentley, M.A. / Paps, J. / Kramer, H.B. / Lee, J. / Aik, W. / Choi, H. / Paulsen, S.M. / Bowman, L.A.H. / Loik, N.D. / Horita, S. / Ho, C.H. / Kershaw, N.J. / Tang, C.M. / Claridge, T.D.W. / Preston, G.M. / McDonough, M.A. / Schofield, C.J.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 8, 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_ref_seq_dif / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein
G: Putative uncharacterized protein
H: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,74224
Polymers205,1268
Non-polymers1,61616
Water10,142563
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8433
Polymers25,6411
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8433
Polymers25,6411
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8433
Polymers25,6411
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8433
Polymers25,6411
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8433
Polymers25,6411
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8433
Polymers25,6411
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8433
Polymers25,6411
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8433
Polymers25,6411
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.330, 62.160, 132.830
Angle α, β, γ (deg.)91.840, 94.700, 90.080
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Putative uncharacterized protein / Prolyl-4-hydroxylase


Mass: 25640.732 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_5159 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88CM1
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 1.82 Å3/Da / Density % sol: 32.33 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M MIB buffer pH 5.0, 25% PEG 1500, 2mM MnCl2, 5mM OGA, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2012
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→62.13 Å / Num. obs: 99718 / % possible obs: 97.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.6
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7268 / % possible all: 96.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å62.13 Å
Translation1.97 Å62.13 Å

-
Processing

Software
NameVersionClassificationNB
SCALA0.1.16data scaling
PHASER2.5.1phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G1M

2g1m


Resolution: 1.97→62.127 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7938 / SU ML: 0.28 / σ(F): 1.96 / Phase error: 28.15 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 1689 2.01 %Random
Rwork0.2118 ---
obs0.2127 99718 94.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.03 Å2 / Biso mean: 34.106 Å2 / Biso min: 8.41 Å2
Refinement stepCycle: LAST / Resolution: 1.97→62.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11194 0 88 563 11845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911602
X-RAY DIFFRACTIONf_angle_d1.04915821
X-RAY DIFFRACTIONf_chiral_restr0.0581667
X-RAY DIFFRACTIONf_plane_restr0.0042110
X-RAY DIFFRACTIONf_dihedral_angle_d15.2694098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.97-1.9940.36721370.314567086845684595
1.994-2.01930.32841280.307468356963696395
2.0193-2.04580.35851570.30967856942694295
2.0458-2.07390.33851320.293970017133713395
2.0739-2.10350.31711540.285165936747674795
2.1035-2.13490.30671310.280169607091709195
2.1349-2.16830.32921350.273467956930693095
2.1683-2.20380.34041400.265867366876687695
2.2038-2.24180.28011390.26267756914691495
2.2418-2.28260.27631450.254967646909690994
2.2826-2.32650.3621520.257967086860686094
2.3265-2.3740.27341320.257967516883688394
2.374-2.42560.31181330.259967266859685995
2.4256-2.4820.33191380.242268326970697094
2.482-2.54410.26811420.243466956837683794
2.5441-2.61290.25311280.22766906818681894
2.6129-2.68980.26541440.23267486892689294
2.6898-2.77660.27281420.222566556797679794
2.7766-2.87580.24741240.218168436967696794
2.8758-2.9910.24481370.218567876924692494
2.991-3.12710.29081440.200666556799679994
3.1271-3.29190.23161420.19767996941694195
3.2919-3.49820.21431290.185768486977697795
3.4982-3.76820.251340.17667756909690995
3.7682-4.14740.19111390.166667986937693795
4.1474-4.74730.21741380.159867466884688495
4.7473-5.98040.23071410.180568496990699096
5.9804-62.15830.22741440.193666346778677893
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9124-0.24180.0721.468-0.11980.7157-0.0814-0.1188-0.40810.0687-0.04730.2780.0349-0.24610.0860.2048-0.00410.06090.18710.020.30987.7689-26.74018.7024
24.21840.0138-1.12851.7458-0.05572.7345-0.0447-0.0197-0.1602-0.0717-0.0871-0.21770.24290.30070.06170.26860.08320.05740.0788-0.02830.40122.3252-38.48013.0412
30.7047-0.48990.12051.0616-0.02930.67540.01380.1179-0.2286-0.33180.00430.12820.08270.074-0.00370.1542-0.02090.03160.1228-0.03190.26813.2744-26.754-2.5862
41.6157-1.16830.21242.6405-0.29660.7281-0.11130.07140.1654-0.06170.0025-0.0463-0.07730.11630.06910.20410.0372-0.01380.3575-0.01330.369332.4656-21.63129.5838
51.35650.70161.71020.37720.82262.4229-0.1140.36160.4737-0.388-0.0057-0.0687-0.40010.28130.07910.2687-0.03190.05890.2371-0.0510.289821.0034-11.4422-0.9998
61.36190.10830.10881.08430.34961.1091-0.1643-0.0176-0.16320.24050.1679-0.0297-0.06680.0939-0.00770.19390.0248-0.0060.1371-0.01080.193720.9818-22.07719.5944
70.99511.03681.46252.98461.52942.15680.04980.036-0.1591-0.06370.06730.23850.1923-0.161-0.04760.2768-0.0352-0.00330.22480.03980.4219-16.0924-33.9194-59.2005
81.023-0.26020.00621.4851-0.02290.72890.068-0.1678-0.02160.0141-0.03520.21010.03280.0094-0.01120.1854-0.02380.01710.0963-0.00560.2381-7.9193-27.6424-54.1115
92.2252-2.19330.86962.1617-0.85780.3409-0.02430.2209-0.0191-0.0492-0.1134-0.16560.19940.14370.09910.36490.07030.00070.3082-0.04320.2345.231-33.7158-68.5041
100.9585-0.61890.13942.4898-0.05610.7223-0.03290.18460.1163-0.34360.04430.2191-0.0293-0.0010.00830.2579-0.0228-0.03840.13680.01810.2295-12.7139-25.9923-65.5895
111.50150.03460.42451.09580.18231.74450.03390.05020.233-0.11090.006-0.0546-0.08480.283-0.06250.147-0.07050.02790.1119-0.00620.17562.5069-21.8853-55.8892
122.81180.2590.75743.497-2.30031.89150.0930.19150.3421-0.3181-0.018-0.1095-0.28830.012-0.04520.6417-0.1981-0.13850.32610.05930.4444-8.7832-14.3987-71.5225
133.8426-2.94675.12736.5415-6.80278.7653-0.1271-0.13420.05530.42030.0738-0.1224-0.31760.18790.09380.4280.083-0.130.2846-0.08510.57358.1158-68.68343.3478
140.81560.2468-0.09511.5703-0.25370.5725-0.01240.1155-0.020.15610.0942-0.3372-0.0373-0.0593-0.04750.1589-0.0052-0.02090.1251-0.00970.25631.1461-59.0459-5.4262
153.30782.29540.75432.13950.26150.29640.0144-0.22830.13070.2161-0.2714-0.053-0.16920.0810.11560.5038-0.03670.02740.30080.01570.3186-13.7837-66.63029.0322
160.47150.21030.31562.16080.42020.25910.0123-0.14780.19510.33840.0757-0.17420.1783-0.00950.0070.42910.011-0.2036-0.1641-0.09990.36395.3833-57.7365.1572
170.921-0.51110.12630.9402-0.57720.76130.0274-0.21080.23130.4791-0.0946-0.0151-0.2134-0.14770.06680.3474-0.00580.00690.2066-0.00170.2206-11.0931-52.12433.1879
181.7294-0.09350.23451.4302-0.19391.25130.0030.00830.22290.22860.0095-0.0665-0.1148-0.1886-0.01430.18590.05420.02150.13610.01170.1694-8.7087-52.5192-4.0592
190.9627-0.57410.23352.3772-0.78120.79860.0666-0.1019-0.3475-0.10590.0191-0.27510.06020.0873-0.01440.246-0.05910.01010.15250.05170.292930.6725-56.0561-66.8837
201.21380.5284-0.35141.6509-0.54011.3730.0966-0.1048-0.2368-0.0976-0.2190.02850.4883-0.17320.05630.3601-0.04990.05390.1513-0.02340.268719.1165-66.8812-65.5617
210.63970.2480.11591.10270.03160.4595-0.0302-0.175-0.09390.24050.0125-0.0920.0823-0.03680.01320.2177-0.01290.03350.12470.02320.268525.1246-57.2869-56.7195
221.10981.3874-0.27463.21190.17570.26520.0792-0.0544-0.04640.0605-0.05740.2040.0267-0.3872-0.02690.1869-0.0639-0.02050.33130.01160.30287.751-50.4779-66.0786
231.50350.0410.37631.3671-0.26611.3343-0.1212-0.0067-0.108-0.34890.03880.1842-0.047-0.20060.07350.21230.0003-0.00740.1315-0.0140.218915.4405-52.7896-69.2929
241.8933-1.62-0.60332.53492.71724.55490.0456-0.11280.20290.0080.04060.2049-0.3213-0.1704-0.06620.5230.1177-0.17840.5012-0.05470.365222.9458-41.8506-46.6671
250.92050.06810.45910.7931-0.34280.50010.07670.0082-0.3268-0.05680.0695-0.02490.5151-0.1903-0.06780.55180.0648-0.09690.37050.02210.3486-11.8859-28.3419-96.8037
260.19670.51120.09292.15760.23690.3262-0.074-0.12820.14550.07940.02340.0318-0.1431-0.1330.02710.43030.05240.04990.5457-0.04430.2703-23.7237-9.035-87.3094
271.9062-0.7008-0.80980.3311-0.16793.5770.1207-0.05540.14340.05730.0731-0.0159-0.1333-0.1085-0.13780.39580.01290.01410.33110.02610.2422-12.1065-4.9067-89.6363
281.2049-0.318-0.1741.47310.39671.3470.0989-0.1665-0.17480.2842-0.0808-0.16910.2816-0.2689-0.02220.6983-0.1057-0.09190.38880.11560.3523-12.5725-24.8238-83.0608
290.98010.0009-0.16821.4658-0.94051.94590.1309-0.1738-0.02310.1433-0.1019-0.1483-0.11670.006-0.02110.33780.0525-0.00570.2082-0.0050.2179-9.8477-9.5831-93.2359
300.8997-0.0289-0.13291.1261-0.24691.22650.08060.0287-0.06490.1329-0.1025-0.15580.15460.06670.02040.27830.0376-0.0270.21930.0230.2245-10.5645-15.5086-97.2533
313.34162.1126-0.45862.7707-1.67994.6528-0.1688-0.1351-0.1910.16160.0691-0.01980.16380.09360.09570.3584-0.07650.15290.38620.01020.56947.5724-65.3492-96.1214
321.1422-0.2331-0.27710.61470.00190.6378-0.2454-0.06390.1159-0.1095-0.0835-0.008-0.1673-0.00640.29770.51380.09110.00110.3296-0.00490.396818.6352-47.2016-101.0131
330.8973-0.8504-0.37591.1731-0.12490.7924-0.064-0.03070.190.03920.0328-0.1354-0.16750.21250.01740.64090.1672-0.04580.4589-0.07170.74686.3858-32.7246-94.3432
340.8104-0.3137-0.38241.41570.84031.1260.04430.09140.03030.0366-0.01530.0517-0.0875-0.05050.0010.67240.095-0.09590.4059-0.10320.453713.4511-41.6914-106.607
351.63250.8373-0.49531.5372-0.51251.0468-0.14240.0356-0.1206-0.105-0.13510.10640.3604-0.39860.18260.6236-0.08450.09150.3945-0.04860.326610.4773-58.3661-108.1617
360.72140.0203-0.22820.92290.00541.1579-0.0154-0.13750.2023-0.2079-0.04350.0076-0.2108-0.1330.03620.32940.05530.0010.3351-0.06510.351910.8234-48.2527-93.9414
370.7533-0.1065-0.32540.0768-0.01270.938-0.11890.2088-0.06680.1120.1472-0.27930.14360.99210.00120.47910.1622-0.04391.12670.01150.2996-11.051-49.8935-33.8797
380.32760.06210.33050.34480.16520.9153-0.12310.0786-0.0733-0.07970.0538-0.13520.17310.6773-0.0330.56640.4066-0.05151.1112-0.00140.1195-16.954-54.5851-43.445
391.23660.582-0.40060.556-0.3270.1954-0.09510.1471-0.052-0.1284-0.0201-0.1686-0.26470.5964-0.03660.1951-0.13880.05920.84830.14130.2351-14.8969-41.047-29.1436
402.3964-0.77480.98542.261-0.51811.0248-0.0011-0.16920.13810.12310.23410.26720.10270.1682-0.08120.22640.10020.02540.70160.00850.229-25.6973-48.4383-35.4504
410.3606-0.0486-0.14960.28140.06270.84830.06280.1854-0.0507-0.1616-0.0764-0.2121-0.06631.10060.11010.06180.17350.02971.12710.0520.2318-12.4102-48.7985-23.9828
420.87430.7355-0.06782.45770.8533.7657-0.09070.1954-0.0121-0.1546-0.19050.13810.0464-0.05930.07680.27980.1415-0.01910.7532-0.01370.132-23.12-50.0281-40.2008
430.2086-0.1040.22260.37780.02180.62650.0962-0.0597-0.129-0.02150.05590.06730.3188-0.25990.13260.8403-0.72490.04490.8836-0.01740.35078.0575-30.2776-29.3703
440.9691-0.4354-0.48032.61980.63890.8788-0.0864-0.1236-0.02010.0858-0.06860.0830.1039-0.06140.06850.34910.03240.08980.9641-0.12410.3673-6.398-18.5214-20.1047
452.42991.788-0.57281.9069-0.58771.5018-0.0199-0.25-0.09150.1282-0.09310.11320.07930.05480.06930.67210.31180.15090.91680.05420.5056-1.3871-3.8792-19.5904
460.4965-0.11520.01280.6633-0.1690.86670.1659-0.0899-0.0312-0.2423-0.33310.18210.2167-1.1291-0.07350.441-0.11920.00520.9516-0.13310.06237.5279-16.3883-20.5
470.71410.311-0.07070.7009-0.38582.767-0.2021-0.02920.06440.1574-0.2148-0.3412-0.1460.25680.26480.1807-0.02610.00110.3964-0.05670.270118.5118-13.4371-27.7099
480.28610.1152-0.0580.06440.08220.8454-0.0123-0.0816-0.0408-0.0156-0.11460.1376-0.0452-1.1650.0125-0.3103-0.17910.1670.8271-0.10810.15836.19-17.3147-32.5404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:31)A1 - 31
2X-RAY DIFFRACTION2(CHAIN A AND RESID 32:45)A32 - 45
3X-RAY DIFFRACTION3(CHAIN A AND RESID 46:114)A46 - 114
4X-RAY DIFFRACTION4(CHAIN A AND RESID 115:123)A115 - 123
5X-RAY DIFFRACTION5(CHAIN A AND RESID 124:134)A124 - 134
6X-RAY DIFFRACTION6(CHAIN A AND RESID 135:206)A135 - 206
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1:10)B1 - 10
8X-RAY DIFFRACTION8(CHAIN B AND RESID 11:41)B11 - 41
9X-RAY DIFFRACTION9(CHAIN B AND RESID 42:75)B42 - 75
10X-RAY DIFFRACTION10(CHAIN B AND RESID 76:107)B76 - 107
11X-RAY DIFFRACTION11(CHAIN B AND RESID 108:199)B108 - 199
12X-RAY DIFFRACTION12(CHAIN B AND RESID 200:203)B200 - 203
13X-RAY DIFFRACTION13(CHAIN C AND RESID 1:6)C1 - 6
14X-RAY DIFFRACTION14(CHAIN C AND RESID 7:41)C7 - 41
15X-RAY DIFFRACTION15(CHAIN C AND RESID 42:75)C42 - 75
16X-RAY DIFFRACTION16(CHAIN C AND RESID 76:105)C76 - 105
17X-RAY DIFFRACTION17(CHAIN C AND RESID 106:128)C106 - 128
18X-RAY DIFFRACTION18(CHAIN C AND RESID 129:202)C129 - 202
19X-RAY DIFFRACTION19(CHAIN D AND RESID 0:23)D0 - 23
20X-RAY DIFFRACTION20(CHAIN D AND RESID 24:45)D24 - 45
21X-RAY DIFFRACTION21(CHAIN D AND RESID 72:113)D72 - 113
22X-RAY DIFFRACTION22(CHAIN D AND RESID 114:127)D114 - 127
23X-RAY DIFFRACTION23(CHAIN D AND RESID 128:200)D128 - 200
24X-RAY DIFFRACTION24(CHAIN D AND RESID 201:207)D201 - 207
25X-RAY DIFFRACTION25(CHAIN E AND RESID 9:31)E9 - 31
26X-RAY DIFFRACTION26(CHAIN E AND RESID 32:53)E32 - 53
27X-RAY DIFFRACTION27(CHAIN E AND RESID 65:75)E65 - 75
28X-RAY DIFFRACTION28(CHAIN E AND RESID 76:106)E76 - 106
29X-RAY DIFFRACTION29(CHAIN E AND RESID 107:127)E107 - 127
30X-RAY DIFFRACTION30(CHAIN E AND RESID 128:203)E128 - 203
31X-RAY DIFFRACTION31(CHAIN F AND RESID 8:20)F8 - 20
32X-RAY DIFFRACTION32(CHAIN F AND RESID 21:62)F21 - 62
33X-RAY DIFFRACTION33(CHAIN F AND RESID 63:68)F63 - 68
34X-RAY DIFFRACTION34(CHAIN F AND RESID 69:78)F69 - 78
35X-RAY DIFFRACTION35(CHAIN F AND RESID 79:105)F79 - 105
36X-RAY DIFFRACTION36(CHAIN F AND RESID 106:201)F106 - 201
37X-RAY DIFFRACTION37(CHAIN G AND RESID 9:73)G9 - 73
38X-RAY DIFFRACTION38(CHAIN G AND RESID 74:109)G74 - 109
39X-RAY DIFFRACTION39(CHAIN G AND RESID 110:126)G110 - 126
40X-RAY DIFFRACTION40(CHAIN G AND RESID 127:140)G127 - 140
41X-RAY DIFFRACTION41(CHAIN G AND RESID 141:194)G141 - 194
42X-RAY DIFFRACTION42(CHAIN G AND RESID 195:203)G195 - 203
43X-RAY DIFFRACTION43(CHAIN H AND RESID 8:28)H8 - 28
44X-RAY DIFFRACTION44(CHAIN H AND RESID 29:44)H29 - 44
45X-RAY DIFFRACTION45(CHAIN H AND RESID 45:53)H45 - 53
46X-RAY DIFFRACTION46(CHAIN H AND RESID 63:120)H63 - 120
47X-RAY DIFFRACTION47(CHAIN H AND RESID 121:135)H121 - 135
48X-RAY DIFFRACTION48(CHAIN H AND RESID 136:202)H136 - 202

+
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