[English] 日本語
Yorodumi
- PDB-4a8h: Crystal structure of putrescine transcarbamylase from Enterococcu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a8h
TitleCrystal structure of putrescine transcarbamylase from Enterococcus faecalis with N-(phosphonoacetyl)-putrescine
ComponentsPUTRESCINE CARBAMOYLTRANSFERASE
KeywordsTRANSFERASE / PAPU / AGMATINE DEIMINASE ROUTE / ORNITHINE / ORNITHINE ARGININE DEIMINASE / PHOSPHONOACETYLPUTRESCINE / PALO
Function / homology
Function and homology information


putrescine carbamoyltransferase / putrescine biosynthetic process from arginine via N-carbamoylputrescine / putrescine carbamoyltransferase activity / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / amino acid binding / cytoplasm
Similarity search - Function
Putrescine carbamoyltransferase PtcA / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold ...Putrescine carbamoyltransferase PtcA / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-(PHOSPHONOACETYL)-PUTRESCINE / Putrescine carbamoyltransferase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPolo, L.M. / Gil-Ortiz, F. / Rubio, V.
CitationJournal: Plos One / Year: 2012
Title: New Insight Into the Transcarbamylase Family: The Structure of Putrescine Transcarbamylase, a Key Catalyst for Fermentative Utilization of Agmatine
Authors: Polo, L.M. / Gil-Ortiz, F. / Cantin, A. / Rubio, V.
History
DepositionNov 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Other
Revision 1.2Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTRESCINE CARBAMOYLTRANSFERASE
B: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,44313
Polymers80,2832
Non-polymers1,16011
Water5,116284
1
A: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules

A: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules

A: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,25821
Polymers120,4243
Non-polymers1,83418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area14450 Å2
ΔGint-61.3 kcal/mol
Surface area36650 Å2
MethodPISA
2
B: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules

B: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules

B: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,07218
Polymers120,4243
Non-polymers1,64715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14030 Å2
ΔGint-64.7 kcal/mol
Surface area36720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.200, 117.200, 225.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1346-

NI

21B-1345-

NI

31B-2015-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEU2AA2 - 732 - 73
21LYSLYSLEULEU2BB2 - 732 - 73
12GLYGLYLYSLYS5AA231 - 244231 - 244
22GLYGLYLYSLYS5BB231 - 244231 - 244
13VALVALALAALA3AA245 - 341245 - 341
23VALVALALAALA3BB245 - 341245 - 341
14GLYGLYTYRTYR2AA76 - 23076 - 230
24GLYGLYTYRTYR2BB76 - 23076 - 230

NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (0.356, -0.934, -0.001), (0.934, 0.356, 0.003), (-0.002, -0.001, 1)
Vector: 10.793, 0.794, 9.217)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein PUTRESCINE CARBAMOYLTRANSFERASE / PTC / PTCASE / AGMATINE CATABOLISM PROTEIN B / PUTRESCINE TRANSCARBAMOYLASE / PUTRESCINE TRANSCARBAMYLASE


Mass: 40141.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q837U7, putrescine carbamoyltransferase

-
Non-polymers , 6 types, 295 molecules

#2: Chemical ChemComp-PUW / N-(PHOSPHONOACETYL)-PUTRESCINE


Mass: 210.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O4P
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.91 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 5.5
Details: 125 MM AMMONIUM SULPHATE, 17% PEG 3350, 0.1 M BIS-TRIS PH 5.5, 0.43 MM N-(PHOSPHONOACETYL)PUTRESCINE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→46 Å / Num. obs: 32509 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21.3 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 35.1
Reflection shellResolution: 2.5→20 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 9.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A1S
Resolution: 2.5→29 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.217 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21651 1637 5 %RANDOM
Rwork0.18225 ---
obs0.184 30779 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å20 Å2
2---0.19 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 66 284 5730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225531
X-RAY DIFFRACTIONr_bond_other_d0.0030.023721
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9747454
X-RAY DIFFRACTIONr_angle_other_deg0.87439115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86125.263266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01615998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6821524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021056
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_it0.2711.53382
X-RAY DIFFRACTIONr_mcbond_other0.0631.51392
X-RAY DIFFRACTIONr_mcangle_it0.54125446
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.01332149
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6044.52008
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
11A426tight positional0.020.05
12B426tight positional0.020.05
31A569tight positional0.10.05
32B569tight positional0.10.05
41A912tight positional0.020.05
42B912tight positional0.020.05
11A582medium positional0.090.5
12B582medium positional0.090.5
21A83medium positional0.120.5
22B83medium positional0.120.5
41A1064medium positional0.10.5
42B1064medium positional0.10.5
21A119loose positional0.415
22B119loose positional0.415
31A737loose positional0.445
32B737loose positional0.445
11A426tight thermal0.040.5
12B426tight thermal0.040.5
31A569tight thermal0.90.5
32B569tight thermal0.90.5
41A912tight thermal0.040.5
42B912tight thermal0.040.5
11A582medium thermal0.052
12B582medium thermal0.052
21A83medium thermal0.262
22B83medium thermal0.262
41A1064medium thermal0.062
42B1064medium thermal0.062
21A119loose thermal0.4210
22B119loose thermal0.4210
31A737loose thermal1.0210
32B737loose thermal1.0210
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 116 -
Rwork0.22 2213 -
obs--100 %
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)
10.97040.5461-0.50642.5976-0.84841.0485-0.01360.1769-0.2088-0.2278-0.0315-0.01830.1312-0.07160.04510.08520.0084-0.00930.0947-0.03870.0522.12946.36921.729
21.44550.06010.23411.1264-1.06641.1095-0.01070.00730.09070.0414-0.0538-0.007-0.07140.00090.06460.06150.0282-0.00880.0979-0.03560.05931.19658.61431.005
32.055-0.3511-2.37051.0308-0.01622.9582-0.0211-0.1536-0.02240.1181-0.027-0.02710.04260.18130.04810.1155-0.0136-0.01710.0802-0.00090.0638-12.48459.88837.889
41.7377-0.09360.50.7094-0.37760.4606-0.0025-0.0785-0.2409-0.04450.03020.07440.0505-0.0435-0.02770.0648-0.00860.02260.03240.00570.07574.65840.81835.674
517.992612.510710.85258.84276.496914.9459-0.1265-0.53620.2312-0.125-0.23750.19910.0177-0.76750.3640.06570.02090.07870.20930.06940.31924.37832.42749.603
61.281-0.31680.18250.89350.02120.7808-0.0389-0.1585-0.10050.1002-0.0052-0.00120.06870.05970.04420.05670.00480.03720.07530.00990.040713.9941.55140.425
71.9224-0.32190.481218.1457-4.92413.55970.07530.3619-0.1861-0.144-0.02510.3274-0.0928-0.1285-0.05020.0894-0.032-0.01470.2373-0.0470.0258-17.85260.00710.927
83.4673-1.0728-0.61362.56064.207622.52950.2201-0.04940.6867-1.2118-0.2440.5149-1.7983-0.41420.02390.60540.1062-0.32860.2174-0.00860.4868-21.70980.39212.122
93.9511-0.1184-1.62551.24170.59291.7882-0.02160.3466-0.1544-0.1576-0.06040.22060.0521-0.24210.0820.0769-0.0119-0.04580.1058-0.00850.052739.45924.30212.639
101.2426-0.2132-1.16781.1239-0.63641.92550.0388-0.14280.0408-0.08860.0470.111-0.0290.0784-0.08580.0484-0.0095-0.0190.05530.00160.033750.85630.22722.417
110.67070.6563-0.2012.51720.26610.17560.0843-0.17120.06290.1558-0.07760.043-0.00360.0682-0.00680.07070.02340.02190.1198-0.00340.067743.44640.03730.124
121.6138-0.3381-0.28141.1831-0.74631.0724-0.03660.0684-0.3626-0.01940.07370.31490.1843-0.2132-0.03710.0733-0.04850.01030.1007-0.00910.171134.34117.45924.967
132.19430.65540.85671.35440.43053.0532-0.1003-0.3976-0.29670.29190.08580.36290.2221-0.33840.01450.17820.00450.10670.19620.12410.278732.86312.84737.479
141.1653-0.39240.09241.3996-0.59041.8451-0.0054-0.0833-0.47590.01290.00980.20780.3961-0.0239-0.00440.1234-0.02550.00660.07840.02660.206643.7258.93828.044
153.91253.0675-0.88133.0714-1.37634.0163-0.09180.21360.1094-0.33590.12140.1892-0.1517-0.1808-0.02960.19440.0837-0.0340.09530.01980.059943.90845.6383.585
1611.0118-3.116312.05771.04-3.030814.1778-0.60080.72240.71-0.03540.2556-0.4135-1.53131.4150.34520.6074-0.41580.37430.6533-0.22920.515862.82758.6823.083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 40
2X-RAY DIFFRACTION2A41 - 69
3X-RAY DIFFRACTION3A70 - 98
4X-RAY DIFFRACTION4A99 - 185
5X-RAY DIFFRACTION5A186 - 194
6X-RAY DIFFRACTION6A195 - 312
7X-RAY DIFFRACTION7A313 - 331
8X-RAY DIFFRACTION8A332 - 340
9X-RAY DIFFRACTION9B1 - 40
10X-RAY DIFFRACTION10B41 - 73
11X-RAY DIFFRACTION11B74 - 112
12X-RAY DIFFRACTION12B113 - 182
13X-RAY DIFFRACTION13B183 - 247
14X-RAY DIFFRACTION14B248 - 308
15X-RAY DIFFRACTION15B309 - 331
16X-RAY DIFFRACTION16B332 - 340

+
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://pdbjlvh1.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