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- PDB-4uqv: methanococcus jannaschii serine hydroxymethyl-transferase in comp... -

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Basic information

Entry
Database: PDB / ID: 4uqv
Titlemethanococcus jannaschii serine hydroxymethyl-transferase in complex with PLP
ComponentsSERINE HYDROXYMETHYLTRANSFERASE
KeywordsTRANSFERASE / SERINE HYDROXYMETHYL-TRANSFERASE
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases / L-allo-threonine aldolase / L-allo-threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process ...Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases / L-allo-threonine aldolase / L-allo-threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / pyridoxal phosphate binding / one-carbon metabolic process / zinc ion binding / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSaccoccia, F. / Angelucci, F. / Ilari, A.
CitationJournal: Proteins / Year: 2014
Title: The Crystal Structure of Archaeal Serine Hydroxymethyltransferase Reveals Idiosyncratic Features Likely Required to Withstand High Temperatures.
Authors: Angelucci, F. / Morea, V. / Angelaccio, S. / Saccoccia, F. / Contestabile, R. / Ilari, A.
History
DepositionJun 25, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionJul 30, 2014ID: 4BHE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: SERINE HYDROXYMETHYLTRANSFERASE
B: SERINE HYDROXYMETHYLTRANSFERASE
C: SERINE HYDROXYMETHYLTRANSFERASE
D: SERINE HYDROXYMETHYLTRANSFERASE
E: SERINE HYDROXYMETHYLTRANSFERASE
F: SERINE HYDROXYMETHYLTRANSFERASE
G: SERINE HYDROXYMETHYLTRANSFERASE
H: SERINE HYDROXYMETHYLTRANSFERASE
I: SERINE HYDROXYMETHYLTRANSFERASE
J: SERINE HYDROXYMETHYLTRANSFERASE
K: SERINE HYDROXYMETHYLTRANSFERASE
L: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)580,76324
Polymers577,79712
Non-polymers2,96612
Water0
1
K: SERINE HYDROXYMETHYLTRANSFERASE
L: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7944
Polymers96,3002
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-64.2 kcal/mol
Surface area26800 Å2
MethodPISA
2
A: SERINE HYDROXYMETHYLTRANSFERASE
B: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7944
Polymers96,3002
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-62.9 kcal/mol
Surface area27540 Å2
MethodPISA
3
C: SERINE HYDROXYMETHYLTRANSFERASE
D: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7944
Polymers96,3002
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-65.2 kcal/mol
Surface area26680 Å2
MethodPISA
4
E: SERINE HYDROXYMETHYLTRANSFERASE
F: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7944
Polymers96,3002
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-58.7 kcal/mol
Surface area27430 Å2
MethodPISA
5
G: SERINE HYDROXYMETHYLTRANSFERASE
H: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7944
Polymers96,3002
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-55 kcal/mol
Surface area27050 Å2
MethodPISA
6
I: SERINE HYDROXYMETHYLTRANSFERASE
J: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7944
Polymers96,3002
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-52.4 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.130, 47.160, 344.079
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SERINE HYDROXYMETHYLTRANSFERASE / / SHMT / SERINE METHYLASE / L-ALLO-THREONINE ALDOLASE


Mass: 48149.758 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): HMS174 (DE3)
References: UniProt: Q58992, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases, L-allo-threonine aldolase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 1.8 Å3/Da / Density % sol: 30.2 % / Description: NONE
Crystal growDetails: (NH)2SO4 1.8M, NH4F 0.1M, 2MM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 3→50 Å / Num. obs: 80852 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 6
Reflection shellResolution: 3→3.18 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1.2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1702)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BHD
Resolution: 3→49.154 Å / σ(F): 1.33 / Phase error: 25.81 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2429 4053 5.01 %
Rwork0.1976 --
obs0.2016 80956 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40190 0 180 0 40370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441282
X-RAY DIFFRACTIONf_angle_d0.9955702
X-RAY DIFFRACTIONf_dihedral_angle_d16.52815410
X-RAY DIFFRACTIONf_chiral_restr0.0375969
X-RAY DIFFRACTIONf_plane_restr0.0047237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.05190.31761970.24723714X-RAY DIFFRACTION94
3.0519-3.10740.28642010.25043813X-RAY DIFFRACTION95
3.1074-3.16710.30022030.25283846X-RAY DIFFRACTION95
3.1671-3.23180.28221970.24463743X-RAY DIFFRACTION95
3.2318-3.3020.31792010.24053826X-RAY DIFFRACTION95
3.302-3.37880.27182040.23433869X-RAY DIFFRACTION95
3.3788-3.46330.28491960.23683738X-RAY DIFFRACTION95
3.4633-3.55690.27052000.22983798X-RAY DIFFRACTION95
3.5569-3.66150.2582040.21973864X-RAY DIFFRACTION95
3.6615-3.77970.25671990.2023782X-RAY DIFFRACTION95
3.7797-3.91470.23042040.19063890X-RAY DIFFRACTION95
3.9147-4.07130.2391970.19143735X-RAY DIFFRACTION95
4.0713-4.25650.21762070.18543929X-RAY DIFFRACTION95
4.2565-4.48080.23391970.1793749X-RAY DIFFRACTION95
4.4808-4.76120.19652060.16943916X-RAY DIFFRACTION95
4.7612-5.12840.22462030.16653863X-RAY DIFFRACTION95
5.1284-5.64370.23162040.18483866X-RAY DIFFRACTION95
5.6437-6.45860.24812060.1963919X-RAY DIFFRACTION95
6.4586-8.13020.20742090.17773962X-RAY DIFFRACTION95
8.1302-46.72880.22982150.18864081X-RAY DIFFRACTION94
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)
10.4313-0.6535-0.22991.88540.59290.5523-0.2013-0.1652-0.11630.10570.03560.18550.0755-0.1603-0.01320.34380.0415-0.03620.37670.00560.04079.260217.684724.8818
20.3861-0.39560.64762.1756-0.77331.0733-0.1781-0.1804-0.1760.24320.19220.2139-0.2017-0.2085-0.00220.31020.15110.02450.37160.03660.20174.59225.420828.8909
31.43840.69110.25391.7931-0.07110.88650.1755-0.1973-0.3110.00110.08080.52380.1958-0.68870.01480.1842-0.0297-0.05040.62460.02280.5757-11.59787.320622.4949
41.0066-0.11070.38481.7766-0.88881.2814-0.038-0.0379-0.0882-0.0233-0.1076-0.4344-0.16450.1187-0.00210.24870.1293-0.00850.2638-0.05640.334526.97929.540820.7661
51.28180.10370.17410.6857-0.59940.50080.06470.10970.0323-0.0634-0.1107-0.206-0.21310.295700.43040.00750.03750.4372-0.05930.384533.625614.969511.2724
61.3236-0.03220.28480.19680.0450.4597-0.23280.72660.4947-0.38120.2478-0.1625-0.2310.29740.00170.6711-0.09690.06010.6947-0.03610.413428.855822.3892-3.9999
70.91760.9214-0.12392.0912-0.37790.8092-0.03020.09660.010.3786-0.0266-0.1819-0.02270.0237-0.00050.28660.1056-0.0310.380.02330.27069.71750.506167.3672
80.5617-0.47020.35452.0030.15790.602-0.08460.1013-0.10040.57830.1209-0.21890.10210.1753-0.00010.54040.0223-0.06710.42580.00540.374417.4414-6.414876.7053
90.5731-0.03170.10963.1029-0.01940.014-0.7438-0.47830.07650.23510.37-0.6265-0.1599-0.3551-0.14410.9603-0.00570.17540.751-0.08830.22247.09-8.477493.2332
101.06580.25530.57712.61960.3870.9569-0.0070.02060.17810.2013-0.11141.03020.1191-0.1398-0.02090.2104-0.01190.17080.36040.07050.5721-10.7112-4.29763.7675
110.295-0.2526-0.2371.4102-0.60530.59620.23460.03610.1273-0.22660.15671.03030.2111-0.17660.17670.1607-0.04410.21310.36640.14541.0503-20.3717-2.670763.4875
121.06310.59420.10010.99350.02130.01020.05790.1630.1320.5297-0.13450.3349-0.1461-0.1129-0.01460.30570.03970.2990.66570.1621.2516-25.121110.177175.8339
131.2356-0.3949-0.08832.77410.2091.0239-0.2143-0.1107-0.21060.2606-0.0270.2045-0.0293-0.0083-0.00190.28620.0365-0.06970.49820.04690.465456.4694-18.712447.2019
140.52030.04090.04670.77770.47270.2850.0248-0.05640.21640.9172-0.18860.4481-0.6884-0.42170.00211.030.0381-0.14680.6226-0.03180.686550.7791-1.099164.5236
150.47390.24410.28530.63160.16950.25020.5546-0.4586-0.08540.1033-0.3112-0.22310.03250.22370.00080.8069-0.122-0.07850.91570.06620.423966.6242-4.035966.0546
160.69460.0761-0.51612.7065-0.4621.06210.00370.0847-0.0097-0.23870.066-0.3553-0.239-0.17060.00040.35880.0178-0.09510.57470.0340.420166.5566-11.504231.3512
170.8583-0.0055-0.44860.76-0.68890.79060.01480.01670.0407-0.677-0.2591-0.2784-0.49180.0893-0.01370.5562-0.0802-0.06350.57440.06350.45372.0088-8.967722.0777
180.8088-0.4395-0.44960.69110.48861.1261-0.26310.0551-0.145-0.1728-0.16-0.3387-0.19880.1397-0.14750.2351-0.1060.17680.75680.20040.846384.2764-26.561325.8343
190.66210.1787-0.30640.8448-0.31461.0035-0.0793-0.11670.05450.19180.2251-0.00770.1818-0.040.00230.2624-0.06480.07120.2707-0.03680.2939-50.55484.1089162.1208
200.6768-0.6806-0.08830.63850.22361.84140.04730.1219-0.0332-0.0901-0.08970.27310.0748-0.23080.00080.3462-0.14870.04570.4321-0.08390.2414-54.9897-4.788136.6667
211.03930.0278-0.23470.9901-0.45021.4843-0.19770.41420.33350.03530.02420.5787-0.0137-0.1974-0.00740.211-0.15540.04380.46170.03880.4552-69.99697.7947150.9938
221.7017-0.2420.05740.6990.57050.461-0.16840.0270.22590.2249-0.03720.1-0.02560.2276-0.07910.4336-0.06660.17110.328-0.02980.1145-49.60363.3726162.6111
231.0497-0.751-0.25550.7129-0.03320.62080.03310.0498-0.1197-0.0986-0.0132-0.3877-0.07870.31330.00360.2741-0.10070.12570.4412-0.00480.4023-29.499112.4174146.3095
240.7820.73720.50041.9255-0.42560.7623-0.08820.1905-0.26330.4635-0.0249-0.65350.02850.2283-0.00110.4254-0.0099-0.08820.443-0.05350.4581-27.2934-0.0847167.0721
251.30870.1143-0.0630.1185-0.17810.24140.19730.16490.6252-0.2805-0.08510.1389-0.3269-0.10790.46970.92860.4382-0.10220.16890.12820.3935-61.109931.610885.1012
261.24071.0010.06082.4459-0.5610.23440.1355-0.1910.1531-0.3678-0.13920.0273-0.22030.30820.0280.25810.0119-0.06090.360.02590.3211-49.896615.1549108.2188
271.30880.34180.14681.9919-1.2161.08-0.0870.12390.1483-0.4314-0.0277-0.25740.0493-0.03970.00190.4753-0.0090.00310.3304-0.0140.2744-45.665425.254792.4313
281.06780.58240.16891.2415-0.07250.9546-0.0482-0.10710.1025-0.3070.12410.192-0.03580.003800.45810.0105-0.10170.32770.01960.4361-70.599422.4766105.5167
290.38560.0069-0.46050.58480.02720.77310.3259-0.3922-0.23260.29030.2293-0.0536-0.5612-0.11110.02770.40370.0061-0.01270.63010.10940.6733-80.196329.9902120.1629
301.38510.4847-0.30011.03920.38070.20120.0664-0.048-0.1855-0.1241-0.10860.0345-0.07450.0095-00.2961-0.0246-0.13510.44020.080.4888-84.936614.355103.8354
310.6784-1.00550.76212.2848-0.09531.6116-0.1456-0.1655-0.1736-0.1484-0.14880.09120.23090.0555-0.00030.3677-0.05270.06320.54420.06870.4434-5.883136.1144124.602
321.1116-0.61670.12490.9388-0.81170.89830.04750.24740.2861-0.2276-0.42770.0672-0.0537-0.0837-0.00330.4698-0.01590.00040.63330.05890.3908-3.818836.457115.1443
331.0118-0.29960.27790.15220.19811.16550.05710.2846-0.2559-0.23230.0142-0.09510.39340.3878-0.00010.76610.1680.07670.70.04370.44550.99520.0037108.2736
340.6363-0.7929-0.26561.06680.02021.1417-0.44730.04170.05750.0964-0.02750.08880.22330.3214-0.00010.4578-0.03560.01550.66450.1740.63714.58735.563127.867
350.6949-0.60510.28890.4829-0.29791.2924-0.0862-0.00670.05830.2471-0.1054-0.0183-0.1411-0.2193-0.00020.56620.03890.02480.56050.00050.47362.755124.7408147.3479
361.44611.3218-0.5551.1855-0.51880.2162-0.1182-0.12320.16020.3718-0.159-0.75340.20380.18860.0060.55070.1045-0.25960.69210.17780.855922.589641.9524149.1333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:161)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 162:292)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 293:429)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:221)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 222:382)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 383:429)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 3:210)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 211:394)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 395:429)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 1:181)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 182:350)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 351:429)
13X-RAY DIFFRACTION13(CHAIN E AND RESID 3:282)
14X-RAY DIFFRACTION14(CHAIN E AND RESID 283:356)
15X-RAY DIFFRACTION15(CHAIN E AND RESID 357:429)
16X-RAY DIFFRACTION16(CHAIN F AND RESID 1:165)
17X-RAY DIFFRACTION17(CHAIN F AND RESID 166:327)
18X-RAY DIFFRACTION18(CHAIN F AND RESID 328:429)
19X-RAY DIFFRACTION19(CHAIN G AND RESID 1:70)
20X-RAY DIFFRACTION20(CHAIN G AND RESID 71:250)
21X-RAY DIFFRACTION21(CHAIN G AND RESID 251:429)
22X-RAY DIFFRACTION22(CHAIN H AND RESID 1:70)
23X-RAY DIFFRACTION23(CHAIN H AND RESID 71:250)
24X-RAY DIFFRACTION24(CHAIN H AND RESID 251:429)
25X-RAY DIFFRACTION25(CHAIN I AND RESID 3:32)
26X-RAY DIFFRACTION26(CHAIN I AND RESID 33:214)
27X-RAY DIFFRACTION27(CHAIN I AND RESID 215:429)
28X-RAY DIFFRACTION28(CHAIN J AND RESID 1:154)
29X-RAY DIFFRACTION29(CHAIN J AND RESID 155:221)
30X-RAY DIFFRACTION30(CHAIN J AND RESID 222:429)
31X-RAY DIFFRACTION31(CHAIN K AND RESID 3:239)
32X-RAY DIFFRACTION32(CHAIN K AND RESID 240:312)
33X-RAY DIFFRACTION33(CHAIN K AND RESID 313:429)
34X-RAY DIFFRACTION34(CHAIN L AND RESID 2:60)
35X-RAY DIFFRACTION35(CHAIN L AND RESID 61:268)
36X-RAY DIFFRACTION36(CHAIN L AND RESID 269:429)

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