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- PDB-3tr9: Structure of a dihydropteroate synthase (folP) in complex with pt... -

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Basic information

Entry
Database: PDB / ID: 3tr9
TitleStructure of a dihydropteroate synthase (folP) in complex with pteroic acid from Coxiella burnetii
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / Biosynthesis of cofactors / prosthetic groups / and carriers
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / tetrahydrofolate biosynthetic process / cytosol
Similarity search - Function
Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PTEROIC ACID / Dihydropteroate synthase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.895 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydropteroate synthase
B: Dihydropteroate synthase
C: Dihydropteroate synthase
D: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,90313
Polymers143,5144
Non-polymers1,3899
Water11,710650
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dihydropteroate synthase
hetero molecules

C: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4868
Polymers71,7572
Non-polymers7296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area4740 Å2
ΔGint-83 kcal/mol
Surface area21090 Å2
MethodPISA
3
B: Dihydropteroate synthase
hetero molecules

D: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4175
Polymers71,7572
Non-polymers6603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area4440 Å2
ΔGint-46 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.877, 86.883, 158.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Dihydropteroate synthase /


Mass: 35878.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_1351, folP / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83BY6, dihydropteroate synthase
#2: Chemical
ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12N6O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M MES pH 5.0, 10% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.895→50 Å / Num. all: 95520 / Num. obs: 95425 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.088 / Χ2: 1.377 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.934.30.60447110.4421100
1.93-1.974.30.49446750.465199.9
1.97-2.014.30.41447460.4751100
2.01-2.054.30.34546960.5091100
2.05-2.094.30.2847310.5431100
2.09-2.144.30.23946850.5731100
2.14-2.194.40.20147320.623199.9
2.19-2.254.40.17647530.631100
2.25-2.324.40.1647190.7111100
2.32-2.394.50.13547450.7691100
2.39-2.484.60.11847860.8351100
2.48-2.584.70.11247170.9161100
2.58-2.74.70.09847651.0431100
2.7-2.844.80.08947571.2221100
2.84-3.024.80.08447881.5031100
3.02-3.254.80.07947941.923199.9
3.25-3.584.70.06847902.301199.9
3.58-4.094.70.05948422.573199.9
4.09-5.166.90.06848962.539199.9
5.16-509.10.07850973.034199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AJ0
Resolution: 1.895→43.442 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8804 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 4782 5.02 %RANDOM
Rwork0.1724 ---
obs0.1743 95310 99.74 %-
all-100352 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.985 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 109.12 Å2 / Biso mean: 29.7166 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.8488 Å2-0 Å20 Å2
2---9.1215 Å20 Å2
3---6.2727 Å2
Refinement stepCycle: LAST / Resolution: 1.895→43.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8539 0 97 650 9286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058814
X-RAY DIFFRACTIONf_angle_d0.91211930
X-RAY DIFFRACTIONf_chiral_restr0.0611349
X-RAY DIFFRACTIONf_plane_restr0.0041547
X-RAY DIFFRACTIONf_dihedral_angle_d12.7443337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8954-1.91690.31671380.27092784292294
1.9169-1.93950.27911590.24930113170100
1.9395-1.96310.26951530.231529843137100
1.9631-1.9880.27871440.215430013145100
1.988-2.01410.25911660.216329853151100
2.0141-2.04170.23841670.196829783145100
2.0417-2.07090.2251620.180430093171100
2.0709-2.10180.21451740.17629653139100
2.1018-2.13460.22381470.164729873134100
2.1346-2.16960.19721450.158430423187100
2.1696-2.2070.19661610.16429483109100
2.207-2.24720.20951490.159430183167100
2.2472-2.29040.22111770.163230163193100
2.2904-2.33710.20521660.160129713137100
2.3371-2.38790.21451600.156830113171100
2.3879-2.44350.19891520.16629883140100
2.4435-2.50460.22131730.163430453218100
2.5046-2.57230.20261470.16430013148100
2.5723-2.6480.21721650.161929973162100
2.648-2.73340.19751700.159930353205100
2.7334-2.83110.2141250.168230423167100
2.8311-2.94440.20461680.173130223190100
2.9444-3.07840.20191640.174430363200100
3.0784-3.24070.22021830.17930123195100
3.2407-3.44360.20121580.170830393197100
3.4436-3.70940.19271510.165430623213100
3.7094-4.08240.19171530.153630733226100
4.0824-4.67260.19561490.149730903239100
4.6726-5.88460.18351710.166131393310100
5.8846-43.45290.23761850.201932373422100
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)
10.17680.03970.07910.07870.05280.25490.01110.1142-0.04810.21910.0489-0.1253-0.08830.18510.0671-0.0802-0.1894-0.3110.1088-0.17050.0358.2954-2.0137.8071
20.58640.0041-0.13530.62910.03460.0360.0001-0.33590.10080.4467-0.0831-0.0887-0.1969-0.00040.0370.29830.04120.04350.2509-0.04090.1409-12.3563-4.662513.0664
30.00890.0393-0.02290.22190.04640.05030.06060.0227-0.03010.20470.04690.09620.01580.0052-0.00920.2248-0.00190.02160.1927-0.00720.2001-7.61142.93844.8914
40.29310.09280.02470.06780.02130.09180.128-0.20340.19390.2638-0.04610.050.0379-0.0530.10790.61350.0718-0.01740.1809-0.13910.1358-8.81947.553314.4365
50.4363-0.0517-0.16340.00720.02210.79850.06240.06410.15840.1203-0.0438-0.2394-0.25170.02740.02440.3014-0.0357-0.06290.1232-0.04490.1829-1.94818.06755.8974
60.1222-0.01840.0570.081-0.11070.19680.0385-0.02230.15340.0793-0.0458-0.011-0.10580.00210.01780.2249-0.036-0.03770.1268-0.00780.2298-2.39735.2336-7.1519
70.42280.0195-0.09350.641-0.11180.5336-0.06280.24020.2503-0.2131-0.0335-0.2395-0.08420.18330.01890.1642-0.04330.02610.2040.01980.24534.0022.8205-14.3219
80.29850.0215-0.00090.3169-0.07970.10370.08170.03840.19290.0015-0.0883-0.13610.00170.03440.00420.1203-0.0304-0.01510.1244-0.00350.17980.08790.0913-5.596
90.1058-0.21190.08350.3638-0.1270.46620.010.02240.0799-0.0309-0.0116-0.05610.03530.07320.0010.1015-0.01110.00940.1121-0.00720.1366-3.7525-12.1927-5.0674
101.10.5757-0.2580.8748-0.55951.8502-0.1719-0.0241-0.09140.1608-0.0958-0.3506-0.1090.05520.14130.1486-0.0203-0.00640.14250.02140.20166.1922-19.51833.0571
110.37390.23750.08750.15550.04780.25650.00230.1294-0.0558-0.24580.09830.1450.1657-0.0841-0.04240.2099-0.0296-0.09270.1419-0.00730.217-19.615815.5494-42.717
120.39860.30010.33340.5645-0.11280.67090.0654-0.01490.2153-0.08420.14070.46660.1001-0.30170.04240.1697-0.0289-0.1320.27630.03870.3452-27.728920.2351-42.8421
130.80830.25490.31590.9204-0.4460.47730.0349-0.19540.05580.04770.15740.51530.0418-0.35990.0870.1432-0.0484-0.13760.27690.03250.36-30.0715.4781-38.2367
140.13670.35210.32270.87630.34481.41560.0608-0.18070.10030.11620.00230.5371-0.0929-0.38460.03130.1359-0.0291-0.01990.201-0.00810.3445-24.11316.0095-25.2865
150.09680.10430.06290.4223-0.21260.30880.0329-0.00690.0060.11310.09460.14240.0343-0.1068-0.05050.132-0.0284-0.0040.1390.01250.173-17.696812.3297-21.069
160.0871-0.1120.05090.1834-0.0530.28850.0373-0.0073-0.01220.00460.02350.06470.0445-0.0002-0.02550.1453-0.006400.1109-0.00270.1247-6.52518.2396-30.836
171.3417-0.1437-0.13960.6130.65290.6918-0.06890.0686-0.2544-0.1613-0.05790.095-0.0815-0.09330.07610.12930.01340.01270.1457-0.03460.1485-2.06567.9522-40.6449
180.1080.02780.04660.76740.16520.5171-0.0195-0.06570.1036-0.2634-0.23040.5742-0.1994-0.1553-0.03340.22180.0767-0.10430.14610.00740.2104-53.8488-2.44232.9081
190.24780.1698-0.03230.26960.2090.4735-0.0617-0.06460.1042-0.4116-0.17570.1238-0.5525-0.06120.07720.37040.0874-0.16630.139-0.01390.29-54.7585.8441-1.0958
200.3483-0.2173-0.21010.67410.27140.7743-0.0141-0.0430.0919-0.12480.0027-0.0497-0.26560.0706-0.05730.1693-0.01190.00190.113-0.0090.1167-38.81033.0298.0719
210.3292-0.0006-0.10370.76040.46510.35930.00570.0169-0.0325-0.0733-0.0116-0.0019-0.01610.02430.0040.12690.00070.00340.13120.00090.0858-42.1381-14.3732.9844
220.06310.0434-0.00010.0985-0.02680.08290.130.05440.2348-0.06390.04970.171-0.2128-0.0925-0.0690.26910.04470.02440.23310.09460.302-23.4501-20.3751-47.3649
230.6743-0.02750.44010.3807-0.04860.2948-0.4099-0.2453-0.0214-0.0066-0.0244-0.10720.11790.04770.13470.38890.04840.09370.2618-0.03630.2731-18.2529-17.4182-26.6966
241.2525-0.0355-0.06750.42180.18470.10340.0106-0.3870.15540.08090.1272-0.0373-0.15770.1333-0.04940.2360.03160.00780.23160.01310.2033-20.5054-25.8649-31.0664
250.08850.09930.07530.1150.10740.3534-0.0709-0.1781-0.00070.0129-0.01340.2523-0.1425-0.0923-0.0710.23510.05640.16960.26830.02220.5615-31.3574-18.7828-27.9608
260.0984-0.1011-0.04730.57350.05780.2676-0.0432-0.1169-0.039-0.06380.04610.4235-0.0066-0.1532-0.00890.23350.04770.07690.28080.00040.5147-31.3247-20.5575-35.1702
270.0394-0.12730.06540.2882-0.01570.1977-0.0407-0.1535-0.00740.13590.11040.6431-0.0291-0.2144-0.07120.19690.00290.01490.26580.07130.4906-28.1918-35.5213-38.3422
280.14020.04890.3821.165-0.32391.2282-0.022-0.0264-0.0964-0.15990.09850.44930.049-0.2315-0.05410.1823-0.0302-0.05030.20830.00760.2633-23.6875-43.8698-46.2173
290.0840.1085-0.130.47420.1180.44660.0373-0.09030.041-0.07980.03250.30440.0249-0.2909-0.06860.1494-0.0207-0.01950.21980.03570.2627-22.7044-34.991-41.5929
300.209-0.0313-0.16730.57150.03980.14350.0508-0.04910.01270.1415-0.04370.07950.01790.0266-0.00380.1352-0.02880.00430.12860.01440.111-9.684-32.9229-39.1822
310.60540.31630.12830.3415-0.33280.93660.0640.24010.25370.01680.07010.0398-0.12920.1638-0.07090.1633-0.01360.00540.21570.01760.1323-5.3035-21.7182-48.4941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 12:35)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 36:60)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 61:83)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 84:103)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 104:139)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 140:167)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 168:189)A0
8X-RAY DIFFRACTION8chain 'A' and (resseq 190:210)A0
9X-RAY DIFFRACTION9chain 'A' and (resseq 211:275)A0
10X-RAY DIFFRACTION10chain 'A' and (resseq 276:293)A0
11X-RAY DIFFRACTION11chain 'B' and (resseq 12:60)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 61:103)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 104:124)B0
14X-RAY DIFFRACTION14chain 'B' and (resseq 125:167)B0
15X-RAY DIFFRACTION15chain 'B' and (resseq 168:210)B0
16X-RAY DIFFRACTION16chain 'B' and (resseq 211:275)B0
17X-RAY DIFFRACTION17chain 'B' and (resseq 276:293)B0
18X-RAY DIFFRACTION18chain 'C' and (resseq 11:60)C0
19X-RAY DIFFRACTION19chain 'C' and (resseq 61:103)C0
20X-RAY DIFFRACTION20chain 'C' and (resseq 104:210)C0
21X-RAY DIFFRACTION21chain 'C' and (resseq 211:292)C0
22X-RAY DIFFRACTION22chain 'D' and (resseq 12:35)D0
23X-RAY DIFFRACTION23chain 'D' and (resseq 36:60)D0
24X-RAY DIFFRACTION24chain 'D' and (resseq 61:85)D0
25X-RAY DIFFRACTION25chain 'D' and (resseq 86:101)D0
26X-RAY DIFFRACTION26chain 'D' and (resseq 102:124)D0
27X-RAY DIFFRACTION27chain 'D' and (resseq 125:167)D0
28X-RAY DIFFRACTION28chain 'D' and (resseq 168:188)D0
29X-RAY DIFFRACTION29chain 'D' and (resseq 189:210)D0
30X-RAY DIFFRACTION30chain 'D' and (resseq 211:275)D0
31X-RAY DIFFRACTION31chain 'D' and (resseq 276:293)D0

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