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- PDB-2v8v: Crystal structure of mutant R322A of beta-alanine synthase from S... -

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Basic information

Entry
Database: PDB / ID: 2v8v
TitleCrystal structure of mutant R322A of beta-alanine synthase from Saccharomyces kluyveri
ComponentsBETA-ALANINE SYNTHASEBeta-ureidopropionase
KeywordsHYDROLASE / DI-ZINC CENTER / AMIDOHYDROLASE / ALPHA AND BETA PROTEIN
Function / homology
Function and homology information


beta-ureidopropionase activity / beta-ureidopropionase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / N-(AMINOCARBONYL)-BETA-ALANINE / Beta-alanine synthase
Similarity search - Component
Biological speciesSACCHAROMYCES KLUYVERI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal Structures of Yeast -Alanine Synthase Complexes Reveal the Mode of Substrate Binding and Large Scale Domain Closure Movements.
Authors: Lundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Yeast Beta-Alanine Synthase Shares a Structural Scaffold and Origin with Dizinc-Dependent Exopeptidases
Authors: Lundgren, S. / Gojkovic, Z. / Piskur, J. / Dobritzsch, D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and Preliminary X-Ray Analysis of Beta-Alanine Synthase from the Yeast Saccharomyces Kluyveri
Authors: Dobritzsch, D. / Gojkovic, Z. / Andersen, B. / Piskur, J.
History
DepositionAug 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-ALANINE SYNTHASE
B: BETA-ALANINE SYNTHASE
C: BETA-ALANINE SYNTHASE
D: BETA-ALANINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,75716
Polymers207,6834
Non-polymers1,07412
Water724
1
A: BETA-ALANINE SYNTHASE
B: BETA-ALANINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2357
Polymers103,8412
Non-polymers3945
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-43.3 kcal/mol
Surface area40540 Å2
MethodPQS
2
C: BETA-ALANINE SYNTHASE
D: BETA-ALANINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5229
Polymers103,8412
Non-polymers6807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-42.6 kcal/mol
Surface area40470 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.478, 84.903, 104.848
Angle α, β, γ (deg.)67.45, 67.81, 62.75
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22D
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A26 - 259
2112B26 - 259
3112C26 - 259
4112D26 - 259
1212A273 - 303
2212B273 - 303
3212C273 - 303
4212D273 - 303
1312A313 - 452
2312B313 - 452
3312C313 - 452
4312D313 - 452
1122A22 - 25
2122D22 - 25
1222A260 - 272
2222D260 - 272
1322A304 - 312
2322D304 - 312
1422A453
2422D453
1132B22 - 25
2132C22 - 25
1234B260 - 272
2234C260 - 272
1334B304 - 312
2334C304 - 312
1434B453
2434C453

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.236, 0.241, -0.941), (0.255, -0.95, -0.179), (-0.938, -0.198, -0.286)-21.83398, -43.52464, -39.02735
2given(0.236, 0.241, -0.941), (0.255, -0.95, -0.179), (-0.938, -0.198, -0.286)-21.83398, -43.52464, -39.02735
3given(0.238, 0.27, -0.933), (0.275, -0.94, -0.202), (-0.932, -0.208, -0.298)-20.52694, -43.94784, -39.76049
4given(0.254, -0.259, 0.932), (-0.244, -0.949, -0.198), (0.936, -0.178, -0.304)-34.51677, 42.11063, 59.23705
5given(0.255, -0.284, 0.924), (-0.279, -0.937, -0.211), (0.926, -0.204, -0.318)-34.16972, 40.84229, 59.2235
6given(0.254, -0.259, 0.932), (-0.244, -0.949, -0.198), (0.936, -0.178, -0.304)-34.51677, 42.11063, 59.23705

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Components

#1: Protein
BETA-ALANINE SYNTHASE / Beta-ureidopropionase


Mass: 51920.691 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-455 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES KLUYVERI (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q96W94, beta-ureidopropionase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-URP / N-(AMINOCARBONYL)-BETA-ALANINE / N-CARBAMYL-BETA-ALANINE / BETA-UREIDOPROPIONATE / 3-Ureidopropionic acid


Mass: 132.118 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8N2O3
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 322 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 322 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ARG 322 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 322 TO ALA ENGINEERED RESIDUE IN CHAIN C, ARG 322 TO ALA ENGINEERED RESIDUE IN CHAIN D, ARG 322 TO ALA
Nonpolymer details1,4-DITHIOTHREITOL (DTT): C 503 IS CONNECTED BY A DISULFIDE BRIDGE TO CYS 168 IN CHAIN C
Sequence detailsTHE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION, THE LAST 20 ...THE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION, THE LAST 20 AMINO ACIDS CORRESPOND TO THE C-TERMINAL HIS-TAG, R322 OF THE DEPOSITED SEQUENCE IS REPLACED BY ALANINE IN THIS MUTANT

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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: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: TRISODIUM CITRATE PH 6.0, DIOXANE,ACETONE, DTT, NA-HEPES PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.874
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.874 Å / Relative weight: 1
ReflectionResolution: 2.9→45 Å / Num. obs: 44094 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R43
Resolution: 2.9→45 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.871 / SU B: 27.409 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2231 5.1 %RANDOM
Rwork0.194 ---
obs0.196 41837 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å21.19 Å20.45 Å2
2---1.14 Å2-2.44 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13355 0 43 4 13402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213736
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.94318583
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82651730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.85924.614635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.344152210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6451565
X-RAY DIFFRACTIONr_chiral_restr0.0950.22015
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.26006
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.29413
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2329
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3191.58751
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.558213754
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.04335630
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7014.54828
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1619tight positional0.050.05
12B1619tight positional0.050.05
13C1619tight positional0.060.05
14D1619tight positional0.060.05
21A108tight positional0.040.05
31B12tight positional0.020.05
11A1495medium positional0.330.5
12B1495medium positional0.350.5
13C1495medium positional0.350.5
14D1495medium positional0.330.5
21A102medium positional0.380.5
31B190medium positional0.270.5
11A1619tight thermal0.060.5
12B1619tight thermal0.060.5
13C1619tight thermal0.060.5
14D1619tight thermal0.060.5
21A108tight thermal0.050.5
31B12tight thermal0.020.5
11A1495medium thermal0.472
12B1495medium thermal0.452
13C1495medium thermal0.442
14D1495medium thermal0.452
21A102medium thermal0.352
31B190medium thermal0.342
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 134
Rwork0.288 2457
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)
115.195815.1956-11.119829.3554-13.73638.6207-0.5180.2975-0.29510.37770.8614-1.1049-0.3583-0.3329-0.3434-0.1085-0.0599-0.06630.1542-0.0445-0.302117.26487.723114.6368
20.5059-0.03440.15470.27080.70431.9507-0.0151-0.05880.01380.0231-0.06240.201-0.0528-0.18120.0775-0.09910.0293-0.0056-0.14980.0469-0.0674-5.04762.61561.9874
30.46190.43841.01911.13071.75273.8083-0.0910.1690.0527-0.25970.0913-0.0138-0.29040.1933-0.0003-0.1363-0.0367-0.0031-0.16080.0473-0.06986.14690.2446-7.2098
43.1438-0.51730.48143.5543-0.0612.6475-0.1925-0.20160.0330.14060.21740.2576-0.026-0.442-0.0249-0.10750.0421-0.0880.03880.02060.0143-31.2117-49.233-38.3758
51.83911.441.67752.41122.24153.1645-0.06910.08150.045-0.15470.06220.04-0.1208-0.04410.007-0.08610.0234-0.0428-0.11690.0307-0.0514-7.7349-31.6582-33.1379
63.87881.85131.97012.3681.4171.7675-0.15190.2963-0.0832-0.2850.1545-0.0631-0.10960.0759-0.0026-0.00810.0594-0.0084-0.1039-0.0008-0.051-11.4239-39.4347-42.1355
710.20955.354-5.81540.8469-6.405826.5442-0.29151.8951-1.3618-1.29740.6737-1.91591.8215-0.0357-0.38220.0308-0.0320.04470.112-0.30960.0266-19.5739-60.5329-57.288
82.90330.4863-0.24793.83860.14332.9705-0.19280.2344-0.0989-0.08010.23710.3470.0691-0.3693-0.0443-0.1347-0.04510.07180.05210.0305-0.0251-69.605454.056724.9937
91.1187-1.3754-0.96892.0811.69411.7979-0.011-0.01660.1080.10750.0628-0.12820.1391-0.1498-0.0518-0.1063-0.04050.0433-0.0537-0.0028-0.0787-46.578139.746419.3592
102.1824-1.9337-1.63173.40982.41852.3392-0.0495-0.25870.18910.10040.1302-0.164-0.04920.1629-0.0807-0.0852-0.0664-0.0202-0.11560.0391-0.0511-44.822342.123522.7659
113.41891.2785-0.38069.66043.76815.8217-0.1369-0.4553-0.19011.00020.19350.04360.41780.1275-0.0566-0.04630.07870.05130.01330.0129-0.1022-63.093450.00738.1961
1213.5813-3.4497-3.18866.20553.82822.4580.625-0.2480.58680.6911-0.5237-0.2819-0.1111.3098-0.1014-0.00860.0548-0.1420.0681-0.11680.066-19.7855-6.1303-25.4929
130.60230.0367-0.04450.39340.77511.80070.04250.049-0.0586-0.02-0.05390.18710.0611-0.22320.0114-0.1059-0.02510.0154-0.12950.0602-0.0884-43.84772.4151-15.8138
140.2433-0.2596-0.87860.88021.16733.2938-0.076-0.16710.00920.21810.0626-0.10190.20180.16670.0133-0.1470.03650.0103-0.12720.04-0.1022-32.61955.2067-6.2909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 34
2X-RAY DIFFRACTION2A130 - 262
3X-RAY DIFFRACTION3A318 - 454
4X-RAY DIFFRACTION4B23 - 218
5X-RAY DIFFRACTION5B219 - 274
6X-RAY DIFFRACTION6B319 - 444
7X-RAY DIFFRACTION7B445 - 453
8X-RAY DIFFRACTION8C23 - 212
9X-RAY DIFFRACTION9C213 - 278
10X-RAY DIFFRACTION10C298 - 419
11X-RAY DIFFRACTION11C420 - 453
12X-RAY DIFFRACTION12D19 - 31
13X-RAY DIFFRACTION13D130 - 261
14X-RAY DIFFRACTION14D318 - 453

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  • 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

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