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- PDB-1n4r: Protein Geranylgeranyltransferase type-I Complexed with a Geranyl... -

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Basic information

Entry
Database: PDB / ID: 1n4r
TitleProtein Geranylgeranyltransferase type-I Complexed with a Geranylgeranylated KKKSKTKCVIL Peptide Product
Components
  • Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
  • Geranylgeranyl transferase type-1 subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE / protein geranylgeranyltransferase type-I / GGTase / geranylgeranyl / protein prenylation / CaaX / lipid modification / rap2b
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / regulation of microtubule-based movement / positive regulation of skeletal muscle acetylcholine-gated channel clustering / acetyltransferase activator activity / heterocyclic compound binding / microtubule associated complex / response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / enzyme-linked receptor protein signaling pathway / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / alpha-tubulin binding / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / positive regulation of cell cycle / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / homeostasis of number of cells within a tissue / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / Signaling by ERBB2 TMD/JMD mutants / female pregnancy / RAF activation / Signaling by SCF-KIT / Signaling by high-kinase activity BRAF mutants
Similarity search - Function
Geranylgeranyl transferase type-1 subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Geranylgeranyl transferase type-1 subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
GERAN-8-YL GERAN / GTPase KRas / Geranylgeranyl transferase type-1 subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTaylor, J.S. / Reid, T.S. / Casey, P.J. / Beese, L.S.
CitationJournal: EMBO J. / Year: 2003
Title: Structure of mammalian protein geranylgeranyltransferase type-I
Authors: Taylor, J.S. / Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S.
History
DepositionNov 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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 / _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: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyl transferase type-1 subunit beta
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
M: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
N: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
O: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
P: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
Q: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
R: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)531,10549
Polymers527,07018
Non-polymers4,03531
Water10,629590
1
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyl transferase type-1 subunit beta
M: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4767
Polymers87,8453
Non-polymers6314
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-71 kcal/mol
Surface area25490 Å2
MethodPISA
2
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
N: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5479
Polymers87,8453
Non-polymers7026
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-95 kcal/mol
Surface area25750 Å2
MethodPISA
3
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
O: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5128
Polymers87,8453
Non-polymers6675
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-82 kcal/mol
Surface area25710 Å2
MethodPISA
4
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
P: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5479
Polymers87,8453
Non-polymers7026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-93 kcal/mol
Surface area25640 Å2
MethodPISA
5
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
Q: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5128
Polymers87,8453
Non-polymers6675
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-86 kcal/mol
Surface area26030 Å2
MethodPISA
6
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
R: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5128
Polymers87,8453
Non-polymers6675
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-82 kcal/mol
Surface area26260 Å2
MethodPISA
7
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9215
Polymers86,5642
Non-polymers3573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9927
Polymers86,5642
Non-polymers4285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9566
Polymers86,5642
Non-polymers3924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
10
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9927
Polymers86,5642
Non-polymers4285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
11
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9566
Polymers86,5642
Non-polymers3924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
12
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9566
Polymers86,5642
Non-polymers3924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)272.068, 268.801, 185.310
Angle α, β, γ (deg.)90.00, 131.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-867-

HOH

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha ...CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha / Type I protein geranyl-geranyltransferase subunit alpha / GGTase-I-alpha


Mass: 44098.145 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: ATCC 63134 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein
Geranylgeranyl transferase type-1 subunit beta / Geranylgeranyl transferase type I subunit beta / GGTase-I-beta / Type I protein geranyl- ...Geranylgeranyl transferase type I subunit beta / GGTase-I-beta / Type I protein geranyl-geranyltransferase subunit beta


Mass: 42466.176 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pggt1b / Plasmid: ATCC 63134 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53610, protein geranylgeranyltransferase type I

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Protein/peptide , 1 types, 6 molecules MNOPQR

#3: Protein/peptide
Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b / KKKSKTKCVIL Peptide Product


Mass: 1280.685 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE GERANYLGERANYL LIPID WAS ADDED BY THE ENZYME.
Source: (synth.) Homo sapiens (human) / References: UniProt: P01116*PLUS

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Non-polymers , 6 types, 621 molecules

#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H34
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 5.47 Å3/Da / Density % sol: 77.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: ammonium sulfate, sodium citrate, dithiothreitol , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
21.3 Mammonium sulfate1reservoir
3175 mM1reservoirpH6.5Na3 citrate
420 mMdithiothreitol1reservoir
5100 mMMES1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.00008 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2001 / Details: toroidal mirror
RadiationMonochromator: Si(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00008 Å / Relative weight: 1
ReflectionResolution: 2.8→29.86 Å / Num. all: 242134 / Num. obs: 242134 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 55.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.432 / % possible all: 98
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 240519 / Num. measured all: 785048 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.432

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.86 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: ncs restraints employed during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.218 12102 5 %RANDOM
Rwork0.2 ---
obs0.2 241366 99.1 %-
all-242097 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.5361 Å2 / ksol: 0.357209 e/Å3
Displacement parametersBiso mean: 54.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.56 Å20 Å2-4.7 Å2
2--11.3 Å20 Å2
3----5.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32304 0 235 590 33129
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 1934 4.9 %
Rwork0.31 37653 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMMES.TOP
X-RAY DIFFRACTION4MES.PARION.TOP
X-RAY DIFFRACTION5GG-CYS.PARGG-CYS.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / Rfactor Rwork: 0.314

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  • 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

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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

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