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- PDB-1rxc: E. COLI uridine phosphorylase: 5-fluorouracil ribose-1-phosphate ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1rxc
TitleE. COLI uridine phosphorylase: 5-fluorouracil ribose-1-phosphate complex
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / pentosyltransferase / uridine phosphorylase / 5-fluorouracil / induced fit / specificity / potassium
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-FLUOROURIDINE / : / PHOSPHATE ION / 1-O-phosphono-alpha-D-ribofuranose / 5-FLUOROURACIL / Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsCaradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium
Authors: Caradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F.
History
DepositionDec 18, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.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 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
G: Uridine phosphorylase
H: Uridine phosphorylase
I: Uridine phosphorylase
J: Uridine phosphorylase
K: Uridine phosphorylase
L: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,70335
Polymers326,26912
Non-polymers3,43423
Water20,6991149
1
A: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,05319
Polymers163,1346
Non-polymers1,91813
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24310 Å2
ΔGint-121 kcal/mol
Surface area45390 Å2
MethodPISA
2
G: Uridine phosphorylase
H: Uridine phosphorylase
I: Uridine phosphorylase
J: Uridine phosphorylase
K: Uridine phosphorylase
L: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,65016
Polymers163,1346
Non-polymers1,51610
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23370 Å2
ΔGint-124 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.188, 191.701, 91.909
Angle α, β, γ (deg.)90.00, 118.50, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is a hexamer. the a.u. contains two hexamers, the first consisting of chains A,B,C,D,E,F and the second of chains G,H,I,J,K,L.

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Components

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Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJKL

#1: Protein
Uridine phosphorylase / / UrdPase / UPase


Mass: 27189.055 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: this structure consists of twelve monomers, nine of which are in the closed conformation (containing substrate, 5-fluorouracil and ribose-1-phosphate) and three are in the open conformation. ...Details: this structure consists of twelve monomers, nine of which are in the closed conformation (containing substrate, 5-fluorouracil and ribose-1-phosphate) and three are in the open conformation. one of the closed active sites (chain j) appears to contain the products of nucleoside synthesis, namely 5-fluorouridine and phosphate. the dimer consisting of chains g and h is the only dimer with both monomers in the open conformation with no concomitant potassium binding.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UDP / Plasmid: pPROEX::pvdS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12758, uridine phosphorylase
#3: Sugar
ChemComp-R1P / 1-O-phosphono-alpha-D-ribofuranose / RIBOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-ribose / 1-O-phosphono-D-ribose / 1-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 1164 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-URF / 5-FLUOROURACIL / Fluorouracil


Mass: 130.077 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication, chemotherapy*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-5UD / 5-FLUOROURIDINE


Mass: 262.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11FN2O6
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1149 / 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: 2.1 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 289 K / Method: batch method under oil / pH: 7.5
Details: TRIS HCL, PEG4000, POTASSIUM ACETATE, 5-FLUOROURACIL, RIBOSE-1-PHOSPHATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 2002 / Details: OSMIC
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→16.93 Å / Num. all: 105171 / Num. obs: 105171 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 6.2
Reflection shellResolution: 2.35→2.47 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.8 / Num. unique all: 13305 / % possible all: 84.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.35→16.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.145 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.808 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 5294 5 %RANDOM
Rwork0.14999 ---
obs0.15267 99877 92.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.214 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.05 Å2
2---0.08 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.242 Å0.249 Å
Luzzati d res low-16.93 Å
Refinement stepCycle: LAST / Resolution: 2.35→16.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22320 0 212 1149 23681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02122904
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221206
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.96131109
X-RAY DIFFRACTIONr_angle_other_deg0.819349151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21152953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.23707
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0225463
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024445
X-RAY DIFFRACTIONr_nbd_refined0.1910.24340
X-RAY DIFFRACTIONr_nbd_other0.2310.226007
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.214280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.21147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.140.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4061.514711
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.757223698
X-RAY DIFFRACTIONr_scbond_it1.01538193
X-RAY DIFFRACTIONr_scangle_it1.7864.57411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 361 -
Rwork0.171 6535 -
obs-6535 83.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83470.38330.08150.80720.00770.8914-0.0001-0.00750.1666-0.09140.01450.2307-0.0704-0.1429-0.01440.10220.0177-0.04140.10730.00010.1798-30.671.12123.794
20.6713-0.14610.10040.77440.07730.7733-0.0189-0.11570.01320.04490.00830.16360.0372-0.05530.01060.0998-0.01580.01550.1395-0.02660.1211-27.431-8.13847.443
30.8015-0.31880.01080.9945-0.47750.8041-0.034-0.14240.07560.2237-0.0494-0.0644-0.02040.04180.08330.1727-0.039-0.02270.1535-0.02410.0618-0.145-3.27861.236
40.91760.2418-0.23460.68290.29950.95780.0408-0.18730.00030.0530.0066-0.1240.08920.1697-0.04740.1052-0.0018-0.04060.17070.00780.104220.504-1.69146.517
50.903-0.0663-0.03430.70520.3530.71060.03530.08140.0776-0.0778-0.0033-0.0589-0.06490.1081-0.0320.148-0.01550.01670.11720.03660.09816.5138.99317.512
60.85420.16630.16560.9712-0.18650.4482-0.02990.10410.08-0.1590.02670.05620.02410.03030.00320.1799-0.0014-0.01610.10570.02420.0897-5.4223.9646.081
71.1512-0.2892-0.20130.7332-0.12380.743-0.0263-0.1007-0.08650.0181-0.0403-0.1109-0.05110.16110.06660.0742-0.022-0.01210.15290.03220.136628.114-48.69820.072
81.33130.587-0.23210.9542-0.31090.6676-0.01740.1331-0.1553-0.0401-0.0729-0.09440.00360.09360.09030.0888-0.00310.01490.1465-0.02650.114622.458-43.864-5.33
90.9818-0.0101-0.16890.55560.21710.5735-0.03690.2205-0.0781-0.06270.0333-0.011-0.0927-0.00060.00360.1328-0.0291-0.00250.1752-0.04820.073-6.433-36.03-12.527
100.7601-0.0387-0.0950.4942-0.03080.6039-0.03480.1059-0.13380.01340.05370.055-0.0129-0.0687-0.01890.1211-0.0082-0.00450.121-0.03560.1374-25.061-44.3692.425
111.0079-0.0487-0.07930.6962-0.04820.4134-0.0253-0.1707-0.15490.05640.01340.0736-0.03340.02920.01190.1309-0.00050.02190.1180.04130.1278-18.451-49.37632.026
120.9864-0.01010.02520.58050.21820.719-0.037-0.2434-0.24910.07450.0447-0.03770.01770.0804-0.00770.10020.0205-0.00420.16180.10.13544.638-56.82738.349
130000000000000000.1436000.143600.1436-0.306-5.6826.941
14-46.2098-20.55721.0788-10.341310.1451.67150.0331-0.13160.27150.11890.08470.3472-0.1807-0.2017-0.11780.14220.0003-0.00050.1416-0.00130.14120.542-0.0275.559
150000000000000000.1436000.143600.1436-25.796-16.28640.675
16-26.4333-1.91-30.4632-13.963219.2057-19.3882-0.00860.6457-0.1371-0.47950.066-0.53890.03790.6363-0.05740.14070.0001-0.00070.13990.00060.1409-29.227-11.941.509
170000000000000000.1436000.143600.143617.312-12.20346.395
180000000000000000.1436000.143600.143618.072-7.60549.831
190000000000000000.1436000.143600.143610.52318.00818.514
20-23.2658-39.3143-5.2295-31.39816.3481-38.576-0.0255-0.3232-0.19190.30670.05580.25920.0353-0.2945-0.03030.1408-0.0007-0.00060.1401-0.00080.140212.0513.87114.763
210000000000000000.1436000.143600.1436-8.638-27.797-5.894
22-34.4372.3158-12.3748-6.175220.8693-13.44840.0027-0.1764-0.17910.20380.0125-0.19450.25120.2698-0.01520.1403-0.000200.14040.00020.1411-11.274-31.778-9.134
23-38.3658.9274-6.7936-4.875.3194-39.4488-0.0040.0523-0.1984-0.1153-0.0307-0.0236-0.07560.07920.03470.14100.00050.142600.1428-21.392-50.672-3.413
240000000000000000.1436000.143600.1436-24.989-46.308-3.432
250000000000000000.1436000.143600.1436-13.184-40.16335.717
26-6.531225.2734-1.32724.97023.5616-7.35530.00480.0794-0.0885-0.0908-0.0070.0770.0809-0.04010.00220.1428-0.00010.00010.1428-0.00030.1422-14.082-45.6637.09
270000000000000000.1436000.143600.1436-0.09-65.12933.134
28-11.51786.233482.2257-4.339427.5838-32.9463-0.01550.2824-0.0115-0.1960.14280.0917-0.36050.3177-0.12730.14110.0036-0.0010.1396-0.00050.143-1.04-61.17937.271
290000000000000000.1436000.143600.14361.9887.79360.051
30-9.68568.8153.7353-3.6164-4.3801-6.498-0.0016-0.0019-0.04890.0021-0.00120.01770.0308-0.01270.00290.1434-0.0001-0.00010.143400.14344.5332.59161.159
310000000000000000.1436000.143600.1436-31.189-3.67635.952
320000000000000000.1436000.143600.143611.52-2.47555.77
330000000000000000.1436000.143600.14366.2836.9599.879
340000000000000000.1436000.143600.1436-17.205-39.57-6.502
350000000000000000.1436000.143600.1436-7.603-53.537.32
360.14160.009-0.01280.04850.02790.0163-0.0090.0002-0.0153-0.00350.00370.0038-0.01660.00520.00530.0603-0.0024-0.01830.06150.01370.0083-2.116-23.46421.296
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 253
2X-RAY DIFFRACTION2B4 - 253
3X-RAY DIFFRACTION3C4 - 253
4X-RAY DIFFRACTION4D4 - 253
5X-RAY DIFFRACTION5E4 - 253
6X-RAY DIFFRACTION6F4 - 253
7X-RAY DIFFRACTION7G4 - 253
8X-RAY DIFFRACTION8H4 - 253
9X-RAY DIFFRACTION9I4 - 253
10X-RAY DIFFRACTION10J4 - 253
11X-RAY DIFFRACTION11K4 - 253
12X-RAY DIFFRACTION12L4 - 253
13X-RAY DIFFRACTION13F2001
14X-RAY DIFFRACTION14F2002
15X-RAY DIFFRACTION15B2011
16X-RAY DIFFRACTION16B2012
17X-RAY DIFFRACTION17D2021
18X-RAY DIFFRACTION18D2022
19X-RAY DIFFRACTION19E2031
20X-RAY DIFFRACTION20E2032
21X-RAY DIFFRACTION21I2041
22X-RAY DIFFRACTION22I2042
23X-RAY DIFFRACTION23J2051
24X-RAY DIFFRACTION24J2052
25X-RAY DIFFRACTION25K2061
26X-RAY DIFFRACTION26K2062
27X-RAY DIFFRACTION27L2071
28X-RAY DIFFRACTION28L2072
29X-RAY DIFFRACTION29C2081
30X-RAY DIFFRACTION30C2082
31X-RAY DIFFRACTION31A2101
32X-RAY DIFFRACTION32C2102
33X-RAY DIFFRACTION33E2103
34X-RAY DIFFRACTION34I2104
35X-RAY DIFFRACTION35K2105
36X-RAY DIFFRACTION36A2102 - 2191
37X-RAY DIFFRACTION36C2103 - 2187
38X-RAY DIFFRACTION36B2013 - 2113
39X-RAY DIFFRACTION36E2104 - 2201
40X-RAY DIFFRACTION36D2023 - 2108
41X-RAY DIFFRACTION36G254 - 342
42X-RAY DIFFRACTION36F2003 - 2098
43X-RAY DIFFRACTION36I2105 - 2199
44X-RAY DIFFRACTION36H254 - 366
45X-RAY DIFFRACTION36K301 - 1147
46X-RAY DIFFRACTION36J2053 - 2172
47X-RAY DIFFRACTION36L2073 - 2156

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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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