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- PDB-3rul: New strategy to analyze structures of glycopeptide-target complexes -

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Basic information

Entry
Database: PDB / ID: 3rul
TitleNew strategy to analyze structures of glycopeptide-target complexes
Components
  • Dalbavancin
  • Ubiquitin
KeywordsSignaling Protein/Antibiotic / antibiotic / glycopeptide / native protein ligation / fusion / carboxymethylation of cysteine / dalbavancin / Signaling Protein-Antibiotic complex
Function / homology
Function and homology information


Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex ...Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Stabilization of p53 / Recognition of DNA damage by PCNA-containing replication complex / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / Negative regulation of FGFR2 signaling / EGFR downregulation / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / G2/M Checkpoints / Negative regulation of FGFR1 signaling / Defective CFTR causes cystic fibrosis / Iron uptake and transport / Negative regulation of NOTCH4 signaling
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
10-METHYLUNDECANOIC ACID / alpha-D-mannopyranose / 2-amino-2-deoxy-beta-D-glucopyranuronic acid / L(+)-TARTARIC ACID / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsEconomou, N.J. / Nahoum, V. / Weeks, S.D. / Grasty, K.C. / Loll, P.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: A carrier protein strategy yields the structure of dalbavancin.
Authors: Economou, N.J. / Nahoum, V. / Weeks, S.D. / Grasty, K.C. / Zentner, I.J. / Townsend, T.M. / Bhuiya, M.W. / Cocklin, S. / Loll, P.J.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Ubiquitin
D: Ubiquitin
E: Dalbavancin
F: Dalbavancin
G: Dalbavancin
H: Dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,89625
Polymers40,9668
Non-polymers2,93017
Water27015
1
A: Ubiquitin
E: Dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1157
Polymers10,2412
Non-polymers8745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
F: Dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1518
Polymers10,2412
Non-polymers9096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin
G: Dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8155
Polymers10,2412
Non-polymers5743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin
H: Dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8155
Polymers10,2412
Non-polymers5743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.300, 86.250, 107.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46
17
27

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resseq 1:16
211chain B and resseq 1:16
311chain C and resseq 1:16
411chain D and resseq 3:15
112chain A and resseq 17:24
212chain B and resseq 17:24
312chain C and resseq 17:24
412chain D and resseq 17:24
113chain A and resseq 26:32
213chain B and resseq 26:32
313chain C and resseq 26:32
413chain D and resseq 26:32
114chain A and resseq 34:39
214chain B and resseq 34:39
314chain C and resseq 34:39
414chain D and resseq 34:39
115chain A and resseq 41:71
215chain B and resseq 41:71
315chain C and resseq 41:71
415chain D and resseq 41:71
116chain A and resseq 74:77
216chain B and resseq 74:77
316chain C and resseq 74:77
416chain D and resseq 74:77
117chain F and resseq 1:7
217chain G and resseq 1:7

NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper:
IDCodeMatrixVector
1given(0.042641, 0.332348, 0.942193), (0.337421, -0.892431, 0.299524), (0.940388, 0.305143, -0.150195)-43.871399, 0.666808, 48.018398
2given(0.290096, 0.319267, 0.902171), (-0.233893, -0.890468, 0.390334), (0.927975, -0.324246, -0.183647)-26.215599, -39.216099, 7.45685
3given(0.804344, -0.593734, -0.022592), (0.59049, 0.803015, -0.080544), (0.065963, 0.051444, 0.996495)-51.0173, 28.845301, 9.31183
4given(0.01953, 0.318639, 0.947675), (0.342244, -0.892724, 0.29311), (0.939408, 0.318611, -0.126487)-44.957001, 0.830295, 47.217201
5given(0.279748, 0.336068, 0.899332), (-0.216497, -0.890524, 0.400121), (0.935345, -0.306636, -0.176365)-26.112801, -39.4147, 7.59471
6given(0.787644, -0.616079, -0.007991), (0.612367, 0.784199, -0.100194), (0.067994, 0.074024, 0.994936)-52.477299, 27.9182, 10.1973
7given(0.016811, 0.311385, 0.950135), (0.309728, -0.905148, 0.291161), (0.950677, 0.289389, -0.111661)-44.9533, -0.066506, 47.7626
8given(0.27034, 0.339946, 0.900751), (-0.248269, -0.879331, 0.406374), (0.930204, -0.333488, -0.15332)-25.796499, -39.091301, 6.83843
9given(0.823752, -0.565994, -0.032909), (0.562263, 0.823013, -0.08069), (0.072754, 0.047965, 0.996196)-49.475601, 30.0385, 8.74839
10given(0.04006, 0.301969, 0.952476), (0.306461, -0.911012, 0.275934), (0.95104, 0.280842, -0.129036)-44.083, 0.298121, 48.352299
11given(0.290098, 0.313157, 0.90431), (-0.275433, -0.877641, 0.392279), (0.916504, -0.362876, -0.168348)-26.6199, -38.732101, 6.45786
12given(0.809319, -0.587332, -0.006598), (0.585279, 0.807336, -0.075205), (0.049498, 0.057004, 0.997146)-50.599701, 29.1301, 9.37592
13given(0.034601, 0.32427, 0.945332), (0.32184, -0.899124, 0.296639), (0.946162, 0.293981, -0.135474)-44.241798, 0.113244, 48.200699
14given(0.278826, 0.334245, 0.900298), (-0.243291, -0.882309, 0.402915), (0.929013, -0.331377, -0.164692)-25.948601, -39.225899, 7.1527
15given(0.796158, -0.60508, 0.00341), (0.602643, 0.79242, -0.094301), (0.054357, 0.077134, 0.995538)-51.5462, 28.389601, 10.4575
16given(0.160661, 0.316142, 0.935009), (0.285563, -0.921689, 0.26257), (0.944797, 0.224819, -0.238358)-41.0406, 0.181438, 51.958302
17given(0.319211, 0.261264, 0.910959), (-0.31404, -0.877774, 0.36179), (0.894138, -0.401564, -0.198147)-29.0989, -37.470699, 6.05066
18given(0.8237, -0.563748, 0.060886), (0.56702, 0.818448, -0.092904), (0.002543, 0.111048, 0.993812)-50.802299, 29.8839, 12.6486
19given(0.804225, -0.59197, 0.052853), (0.594302, 0.800239, -0.080135), (0.005143, 0.095857, 0.995382)-52.039398, 27.682501, 11.7917

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Ubiquitin


Mass: 8952.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein/peptide
Dalbavancin


Mass: 1289.175 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Sugars , 2 types, 8 molecules

#5: Sugar
ChemComp-N1L / 2-amino-2-deoxy-beta-D-glucopyranuronic acid / 2-amino-2-deoxy-beta-D-glucuronic acid / 2-amino-2-deoxy-D-glucuronic acid / 2-amino-2-deoxy-glucuronic acid


Type: D-saccharide, beta linking / Mass: 193.155 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H11NO6
IdentifierTypeProgram
b-D-GlcpANIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 24 molecules

#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-M12 / 10-METHYLUNDECANOIC ACID


Mass: 200.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsDALBAVANCIN IS A TETRACYCLIC LIPOGLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE ...DALBAVANCIN IS A TETRACYCLIC LIPOGLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY MONSACCHARIDES 2-AMINO-2-DEOXY-BETA- D-GLUCOPYRANURONIC ACIDRISTOSAMINE AND D-MANNOSE AND HAS FATTY ACID METHYLUNDECANOIC ACID. HERE, DALBAVANCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE THREE LIGANDS (HET) MAN, N1L, AND M12. GROUP: 1 NAME: DALBAVANCIN CHAIN: E, F, G, H COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7 COMPONENT_2: SUGAR (2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANURONIC ACID) COMPONENT_3: SUGAR (ALPHA-D-MANNOSE) COMPONENT_4: METHYLUNDECANOIC ACID DESCRIPTION: DALBAVANCIN IS A TETRACYCLIC LIPOGLYCOPEPTIDE, GLYCOSYLATED BY A MONOSACCHARIDE ON RESIDUE 4 (RESIDUE 8), AND A MONOSACCHARIDE ON RESIDUE 7 (RESIDUE 9) AND HAS FATTY ACID METHYLUNDECANOIC ACID (RESIDUE 10).
Sequence detailsTHE AUTHORS STATE THAT THESE RESIDUES ARE LIGATED NON-RECOMBINANTLY WITH NATIVE PROTEIN LIGATION ...THE AUTHORS STATE THAT THESE RESIDUES ARE LIGATED NON-RECOMBINANTLY WITH NATIVE PROTEIN LIGATION AFTER PROTEIN EXPRESSION AND PURIFICATION.

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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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9537 Å
DetectorDate: Mar 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→19.6 Å / Num. all: 17703 / Num. obs: 16489 / % possible obs: 93.14 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16 % / Biso Wilson estimate: 50.76 Å2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å19.65 Å
Translation2.6 Å19.65 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ANJ

3anj


Resolution: 2.5→19.603 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.99 / Phase error: 31.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 907 5.14 %
Rwork0.2428 --
obs0.2445 17635 99.88 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.82 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--21.8954 Å20 Å2-0 Å2
2--40.7618 Å20 Å2
3----18.8663 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 189 15 3060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083112
X-RAY DIFFRACTIONf_angle_d1.2854236
X-RAY DIFFRACTIONf_dihedral_angle_d13.911268
X-RAY DIFFRACTIONf_chiral_restr0.083484
X-RAY DIFFRACTIONf_plane_restr0.008536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A126X-RAY DIFFRACTIONPOSITIONAL
12B126X-RAY DIFFRACTIONPOSITIONAL0.036
13C126X-RAY DIFFRACTIONPOSITIONAL0.034
14D100X-RAY DIFFRACTIONPOSITIONAL0.038
21A61X-RAY DIFFRACTIONPOSITIONAL
22B61X-RAY DIFFRACTIONPOSITIONAL0.023
23C61X-RAY DIFFRACTIONPOSITIONAL0.028
24D61X-RAY DIFFRACTIONPOSITIONAL0.021
31A55X-RAY DIFFRACTIONPOSITIONAL
32B55X-RAY DIFFRACTIONPOSITIONAL0.037
33C55X-RAY DIFFRACTIONPOSITIONAL0.035
34D55X-RAY DIFFRACTIONPOSITIONAL0.027
41A43X-RAY DIFFRACTIONPOSITIONAL
42B43X-RAY DIFFRACTIONPOSITIONAL0.037
43C43X-RAY DIFFRACTIONPOSITIONAL0.033
44D43X-RAY DIFFRACTIONPOSITIONAL0.032
51A252X-RAY DIFFRACTIONPOSITIONAL
52B252X-RAY DIFFRACTIONPOSITIONAL0.032
53C252X-RAY DIFFRACTIONPOSITIONAL0.034
54D252X-RAY DIFFRACTIONPOSITIONAL0.027
61A30X-RAY DIFFRACTIONPOSITIONAL
62B30X-RAY DIFFRACTIONPOSITIONAL0.033
63C30X-RAY DIFFRACTIONPOSITIONAL0.03
64D30X-RAY DIFFRACTIONPOSITIONAL0.036
71F84X-RAY DIFFRACTIONPOSITIONAL
72G84X-RAY DIFFRACTIONPOSITIONAL0.088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65630.37711580.32072710X-RAY DIFFRACTION100
2.6563-2.86080.34481590.31952736X-RAY DIFFRACTION100
2.8608-3.14760.35971720.29262747X-RAY DIFFRACTION100
3.1476-3.60070.26831500.27912762X-RAY DIFFRACTION100
3.6007-4.52720.27421340.222817X-RAY DIFFRACTION100
4.5272-19.60320.21811340.20222956X-RAY DIFFRACTION100

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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