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- PDB-1ogy: Crystal structure of the heterodimeric nitrate reductase from Rho... -

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Basic information

Entry
Database: PDB / ID: 1ogy
TitleCrystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides
Components
  • DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
  • PERIPLASMIC NITRATE REDUCTASE
KeywordsOXIDOREDUCTASE / NITRATE REDUCTASE
Function / homology
Function and homology information


nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / molybdenum ion binding / anaerobic respiration / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity ...nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / molybdenum ion binding / anaerobic respiration / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / metal ion binding
Similarity search - Function
Phosphorylase Kinase; domain 1 - #210 / Nitrate reductase cytochrome c-type subunit NapB / Nitrate reductase cytochrome c-type subunit (NapB) / Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Molybdopterin oxidoreductase, molybdopterin cofactor binding site ...Phosphorylase Kinase; domain 1 - #210 / Nitrate reductase cytochrome c-type subunit NapB / Nitrate reductase cytochrome c-type subunit (NapB) / Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Multiheme cytochrome c family profile. / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Multiheme cytochrome superfamily / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Phosphorylase Kinase; domain 1 / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HEME C / Chem-MGD / MOLYBDENUM ATOM / IRON/SULFUR CLUSTER / Periplasmic nitrate reductase / Periplasmic nitrate reductase, electron transfer subunit
Similarity search - Component
Biological speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsArnoux, P. / Sabaty, M. / Alric, J. / Frangioni, B. / Guigliarelli, B. / Adriano, J.-M. / Pignol, D.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase
Authors: Arnoux, P. / Sabaty, M. / Alric, J. / Frangioni, B. / Guigliarelli, B. / Adriano, J.-M. / Pignol, D.
#1: Journal: Biochemistry / Year: 2002
Title: The 1.25 A Resolution Structure of the Diheme Napb Subunit of Soluble Nitrate Reductase Reveals a Novel Cytochrome C Fold with a Stacked Heme Arrangement
Authors: Brige, A. / Leys, D. / Meyer, T.E. / Cusanovich, M.A. / Van Beeumen, J.J.
#2: Journal: Structure / Year: 1999
Title: Crystal Structure of the First Dissimilatory Nitrate Reductase (Nap) at 1.9 A Solved by MAD Methods
Authors: Dias, J.M. / Than, M. / Humm, A. / Huber, R. / Bourenkov, G. / Bartunik, H. / Bursakov, S. / Calvete, J. / Caldeira, J. / Carneiro, C. / Moura, J. / Moura, I. / Romao, M.J.
History
DepositionMay 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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_conn_type
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_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_label_atom_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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "KF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "OG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMIC NITRATE REDUCTASE
B: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
C: PERIPLASMIC NITRATE REDUCTASE
D: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
E: PERIPLASMIC NITRATE REDUCTASE
F: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
G: PERIPLASMIC NITRATE REDUCTASE
H: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
I: PERIPLASMIC NITRATE REDUCTASE
J: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
K: PERIPLASMIC NITRATE REDUCTASE
L: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
M: PERIPLASMIC NITRATE REDUCTASE
N: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
O: PERIPLASMIC NITRATE REDUCTASE
P: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)862,96664
Polymers837,64016
Non-polymers25,32648
Water0
1
A: PERIPLASMIC NITRATE REDUCTASE
B: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8718
Polymers104,7052
Non-polymers3,1666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PERIPLASMIC NITRATE REDUCTASE
D: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8718
Polymers104,7052
Non-polymers3,1666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: PERIPLASMIC NITRATE REDUCTASE
F: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8718
Polymers104,7052
Non-polymers3,1666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: PERIPLASMIC NITRATE REDUCTASE
H: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8718
Polymers104,7052
Non-polymers3,1666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
I: PERIPLASMIC NITRATE REDUCTASE
J: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8718
Polymers104,7052
Non-polymers3,1666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
K: PERIPLASMIC NITRATE REDUCTASE
L: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8718
Polymers104,7052
Non-polymers3,1666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
M: PERIPLASMIC NITRATE REDUCTASE
N: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8718
Polymers104,7052
Non-polymers3,1666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
O: PERIPLASMIC NITRATE REDUCTASE
P: DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8718
Polymers104,7052
Non-polymers3,1666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.000, 225.200, 154.600
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.90068, 0.30378, -0.31063), (0.3149, -0.03618, -0.94844), (-0.29935, -0.95206, -0.06307)26.3558, 141.157, 152.48648
2given(-0.99995, -0.00918, -0.00385), (0.00939, -0.99835, -0.0567), (-0.00332, -0.05673, 0.99838)50.95316, 218.29327, 6.28691
3given(0.90453, -0.27156, -0.32877), (-0.31148, 0.10579, -0.94435), (0.29123, 0.95659, 0.0111)44.40434, 141.14537, -72.44903
4given(-0.90698, 0.27488, 0.31911), (0.29225, -0.13487, 0.94679), (0.30329, 0.95197, 0.04199)4.9496, 78.56278, -73.14667
5given(0.81387, -0.58061, -0.02261), (-0.58065, -0.81414, 0.00541), (-0.02155, 0.00872, -0.99973)68.41241, 210.24144, 77.56707
6given(-0.81028, 0.58564, 0.02153), (0.58601, 0.80934, 0.03937), (0.00563, 0.04451, -0.99899)-19.67288, 4.42967, 73.00153
7given(0.91353, -0.29044, 0.28479), (-0.27623, 0.07097, 0.95847), (-0.29859, -0.95426, -0.01539)22.70364, 70.0268, 150.88237

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Components

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Protein , 2 types, 16 molecules ACEGIKMOBDFHJLNP

#1: Protein
PERIPLASMIC NITRATE REDUCTASE / NITRATE REDUCTASE


Mass: 90114.625 Da / Num. of mol.: 8 / Fragment: CATALYTIC SUBUNIT, RESIDUES 30-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: Q53176, nitrate reductase
#2: Protein
DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE


Mass: 14590.408 Da / Num. of mol.: 8 / Fragment: CYTOCHROME SUBUNIT, RESIDUES 25-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: Q53177

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Non-polymers , 4 types, 48 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mo
#5: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growMethod: vapor diffusion / pH: 8.2
Details: VAPOUR-DIFFUSION. MIXING EQUAL AMOUNTS OF PROTEIN 25MG/ML., pH 8.20
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 %bis-Tris-propane1reservoirpH8.2
210 %(v/v)glycerol1reservoir
315 %(w/v)PEG40001reservoir
415 mM1reservoirNaN3
525 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 134043 / % possible obs: 97.1 % / Redundancy: 2 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.3
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.8 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 30 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
Highest resolution: 3.2 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2NAP, 1JNI

2nap

1jni


Resolution: 3.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE ARE 8 HETERODIMERS IN THE ASU BUT THE PHYSIOLOGICAL UNIT IS ONE HETERODIMER. RESTRAINTS HAD BEEN RELEASED IN THE LAST REFINEMENT STEP. HETERODIMER WITH CHAIN ID A AND B IS THE COMPLEX ...Details: THERE ARE 8 HETERODIMERS IN THE ASU BUT THE PHYSIOLOGICAL UNIT IS ONE HETERODIMER. RESTRAINTS HAD BEEN RELEASED IN THE LAST REFINEMENT STEP. HETERODIMER WITH CHAIN ID A AND B IS THE COMPLEX HAVING THE LOWEST TEMPERATURE FACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1347 1 %RANDOM
Rwork0.2504 ---
obs0.2504 134043 97.1 %-
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.193 Å20 Å2-1.598 Å2
2--3.831 Å20 Å2
3---4.362 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57824 0 1512 0 59336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.86
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.2→3.24 Å / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.369 47 1 %
Rwork0.334 5006 -
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Rfactor Rfree: 0.269 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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