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- PDB-3pcr: Structure of EspG-Arf6 complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3pcr
TitleStructure of EspG-Arf6 complex
Components
  • ADP-ribosylation factor 6
  • EspG
KeywordsPROTEIN TRANSPORT / BACTERIAL EFFECTOR / SMALL G PROTEIN / SMALL GTP-BINDING PROTEIN / ARF / ADP-RIBOSYLATION FACTOR 6
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / ruffle assembly / positive regulation of keratinocyte migration / regulation of filopodium assembly / positive regulation of focal adhesion disassembly / MET receptor recycling / endocytic recycling / thioesterase binding / Flemming body / filopodium membrane / TBC/RABGAPs / protein localization to cell surface / cortical actin cytoskeleton organization / hepatocyte apoptotic process / positive regulation of actin filament polymerization / cleavage furrow / endocytic vesicle / synaptic vesicle endocytosis / regulation of presynapse assembly / vesicle-mediated transport / ruffle / signaling adaptor activity / small monomeric GTPase / positive regulation of protein secretion / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / intracellular protein transport / liver development / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / recycling endosome membrane / GDP binding / nervous system development / presynapse / Clathrin-mediated endocytosis / G protein activity / midbody / early endosome membrane / cell cortex / cell differentiation / postsynapse / cell adhesion / endosome / cell division / cysteine-type endopeptidase activity / focal adhesion / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
EspG protein, N-terminal domain / Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / ADP-ribosylation factor 6 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family ...EspG protein, N-terminal domain / Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / ADP-ribosylation factor 6 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Nuclear Transport Factor 2; Chain: A, / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / ADP-ribosylation factor 6 / T3SS secreted effector EspG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsTomchick, D.R. / Alto, N.M. / Selyunin, A.S.
CitationJournal: Nature / Year: 2011
Title: The assembly of a GTPase-kinase signalling complex by a bacterial catalytic scaffold.
Authors: Selyunin, A.S. / Sutton, S.E. / Weigele, B.A. / Reddick, L.E. / Orchard, R.C. / Bresson, S.M. / Tomchick, D.R. / Alto, N.M.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 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 / struct_conn / 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_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_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.pdbx_leaving_atom_flag / _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_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_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: EspG
B: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4434
Polymers58,8952
Non-polymers5472
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-23 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.566, 104.566, 98.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein EspG / EspG protein


Mass: 40033.488 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs4590, espG, Z5142 / Plasmid: pPRO-EX-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DB50
#2: Protein ADP-ribosylation factor 6


Mass: 18861.986 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 14-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF6 / Plasmid: pPRO-EX-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62330
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2% PEG 4000, 0.1 M sodium acetate, 5% 2,3-methylpentanediol, pH 5.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97956, 0.97989, 0.97188
DetectorType: SBC-3 / Detector: CCD / Date: Dec 16, 2009 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979561
20.979891
30.971881
ReflectionResolution: 2.5→50 Å / Num. obs: 34977 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.05 / Χ2: 0.99 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.549.80.839490.9671100
2.54-2.599.70.7329380.971100
2.59-2.649.80.6049500.9561100
2.64-2.699.80.4749650.9611100
2.69-2.759.70.3949560.9621100
2.75-2.829.80.3229500.9221100
2.82-2.899.70.2669560.9841100
2.89-2.969.70.2179530.9561100
2.96-3.059.70.1619570.9921100
3.05-3.159.70.1199481.0191100
3.15-3.269.70.0959731.0261100
3.26-3.399.70.0749661.0511100
3.39-3.559.70.069581.0331100
3.55-3.739.60.059771.1291100
3.73-3.979.60.0439721.062199.9
3.97-4.279.50.0369751.002199.9
4.27-4.79.50.0329920.977199.8
4.7-5.389.40.0319940.93199.8
5.38-6.789.10.03110110.94199.6
6.78-508.10.02910720.959197

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.001 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7427 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
Details: THE HIGHER-THAN-AVERAGE RFREE VALUE IS PROBABLY DUE TO THE RELATIVE DEARTH OF LATTICE CONTACTS FOR THE ARF6 MOLECULE, AS EVIDENCED BY WEAK ELECTRON DENSITY FOR THE PORTIONS OF ARF6 THAT ARE ...Details: THE HIGHER-THAN-AVERAGE RFREE VALUE IS PROBABLY DUE TO THE RELATIVE DEARTH OF LATTICE CONTACTS FOR THE ARF6 MOLECULE, AS EVIDENCED BY WEAK ELECTRON DENSITY FOR THE PORTIONS OF ARF6 THAT ARE DISTAL TO THE ESPG-BINDING SITE. THE DENSITY FOR THE PORTIONS OF ARF6 THAT ARE PROXIMAL TO ESPG AND THE MG2+-GTP IS STRONG AND WELL CONNECTED
RfactorNum. reflection% reflectionSelection details
Rfree0.3264 1804 5.16 %RANDOM
Rwork0.2228 ---
all0.2278 34977 --
obs0.2278 34977 97.36 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.73 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 258.54 Å2 / Biso mean: 64.0262 Å2 / Biso min: 5.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.8779 Å20 Å20 Å2
2--0.8779 Å2-0 Å2
3----1.7557 Å2
Refine analyzeLuzzati sigma a obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 33 134 4167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154113
X-RAY DIFFRACTIONf_angle_d1.2655601
X-RAY DIFFRACTIONf_chiral_restr0.081638
X-RAY DIFFRACTIONf_plane_restr0.005720
X-RAY DIFFRACTIONf_dihedral_angle_d17.2441543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.59040.43361520.30852620277278
2.5904-2.69410.41412180.28393272349097
2.6941-2.81660.36772040.270333893593100
2.8166-2.96490.47521840.278834073591100
2.9649-3.15050.33671690.238134063575100
3.1505-3.39340.29581870.236134143601100
3.3934-3.73420.31961790.217534083587100
3.7342-4.27310.32251840.190833953579100
4.2731-5.37810.24681690.180834353604100
5.3781-29.00330.29611580.206334273585100
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)
10.86920.2655-0.83480.8523-0.39361.68080.210.37920.3839-0.3302-0.3317-0.231-0.0370.39250.05580.0141-0.00740.01450.190.15110.2607-10.5743-2.0037-22.2513
20.81950.3980.50760.32790.42421.01320.3318-0.0667-0.00420.0398-0.2199-0.14860.01360.17560.44170.1331-0.00470.07610.22960.23310.2623-17.2618-0.5503-14.534
30.28210.02-0.0040.2418-0.04130.13020.12210.16490.0351-0.1322-0.0940.1839-0.1019-0.0596-0.0201-0.0293-0.12340.19310.03840.36390.1321-25.63456.0643-23.0193
40.18730.1172-0.11480.1551-0.12480.09620.18320.0309-0.16780.0226-0.1151-0.0011-0.0812-0.01410.2582-0.1331-0.62360.48-0.26320.53750.2005-16.01447.3006-23.3994
52.32210.64520.22760.98141.11711.58870.44960.57360.0894-0.02440.1372-0.2634-0.0986-0.3688-0.26230.14190.07230.03590.10920.11210.3304-27.4688-8.1912-23.2255
61.10730.4870.14970.66350.84621.37390.62180.1689-0.30430.04620.0499-0.74920.60640.1082-0.580.52230.1036-0.12580.6552-0.07180.9228-15.655-20.7843-14.4513
71.8240.17281.4111.42570.84482.26250.7485-0.5568-0.29020.2235-0.3307-0.45830.7209-0.8099-0.5350.147-0.047-0.1441-0.03820.29290.3368-27.0427-12.3953-12.9761
80.38870.2643-0.1490.99290.11830.09490.3827-0.3202-0.08880.6698-0.0184-0.39530.355-0.2148-0.1070.1801-0.3274-0.00890.12470.4270.0523-32.5205-8.2092.1838
91.91120.94740.00970.62490.08051.69560.6083-0.89990.01850.4636-0.43420.09940.0421-0.7038-0.30690.2595-0.21460.04720.31320.14620.1303-29.7952-0.7785.3746
100.660.27610.20620.1210.04381.26440.1231-0.1764-0.4757-0.1193-0.097-0.4840.8732-0.4199-0.28190.4909-0.2149-0.21570.08350.18240.5295-30.9563-28.5804-12.1328
110.28-0.0444-0.27070.03640.17410.820.2087-0.5356-0.0909-0.340.13960.2884-0.1375-0.3637-0.11930.2072-0.1321-0.23770.09230.18620.2133-28.3272-2.2508-4.716
121.1120.6470.52190.4515-0.05832.14510.3604-0.1588-0.5475-0.05080.1555-0.24110.78590.0466-0.1280.2408-0.1219-0.14170.10830.13490.2754-29.9153-17.1234-15.5614
131.06670.299-0.29860.8337-0.08481.71920.4966-0.1782-0.3024-0.0025-0.09080.00590.2094-0.42310.6020.0855-0.15180.00550.22210.24740.1651-35.7534-6.1873-8.7009
141.2684-0.8363-1.19292.04080.36361.24220.4740.4486-0.1475-0.9035-0.17950.43260.2853-1.5165-0.41571.16490.4131-0.47051.96820.04620.1648-43.2649-15.9201-44.6728
151.3420.322-0.78940.3123-0.32872.96230.268-0.10410.0868-0.25470.36630.16150.5377-1.5949-0.36050.2588-0.2297-0.20220.66660.21890.1624-39.5392-18.6801-33.2827
161.3059-1.80130.80242.8651-1.41282.8950.57120.13390.0811-0.43950.48630.1474-0.1971-1.7538-0.69480.32050.1692-0.05770.61740.43410.3183-39.1977-12.5641-32.0515
171.7698-0.0320.1091.9049-1.03630.64620.0807-0.1160.1546-0.69220.76250.3990.7474-1.7299-1.09180.5260.193-0.04111.07670.4760.417-38.7568-16.0802-42.6603
180.04270.0178-0.05990.0088-0.02610.0815-0.0885-0.3489-0.0970.07250.04960.0820.0489-0.01870.03020.82460.4006-0.29771.92210.42071.3454-55.0566-10.9137-33.79
190.3386-0.03020.08670.82880.40260.28730.58580.1418-0.0415-0.5212-1.0973-0.2352-0.2267-1.07620.37030.97220.121-0.44081.37840.38640.568-49.2035-15.3634-42.9547
206.64622.61711.22072.7711.26840.88650.3523-0.4220.32560.4873-0.6077-0.11150.6765-0.65880.24861.1347-0.893-0.1121.4495-0.11660.6807-53.4712-27.6432-26.988
210.11090.005-0.00660.0056-0.01920.0550.0561-0.35630.1737-0.0364-0.08450.13480.0615-0.273-0.00260.7323-0.0732-0.32181.8286-0.0671.3251-59.5966-22.5783-35.4163
223.0338-0.2938-1.08374.15470.78431.41120.2374-0.13340.6403-1.15620.00720.2148-0.42010.0527-0.33051.1999-0.366-0.50770.98740.61131.2496-57.1764-15.1218-48.0474
230.0118-0.00160.00770.01520.02260.03150.4370.34480.11010.55-0.0262-0.05650.4954-0.2434-0.30520.9829-0.0589-0.28841.512-0.08450.5275-47.3541-25.3564-41.4517
241.17251.5804-1.57613.0239-2.55963.05450.5913-0.4292-0.32710.2263-0.50410.02210.3634-0.2619-0.17511.4027-0.5706-0.42391.090.26920.6273-46.749-34.6655-28.2631
250.41920.68730.86241.96520.42463.9068-0.62320.32450.4738-0.49410.13610.4778-0.8680.56930.47521.6127-1.0218-0.67251.20240.05651.4027-54.1481-35.1449-36.5576
260.04030.1342-0.09050.5104-0.39930.33450.08240.0278-0.10640.2456-0.2598-0.128-0.0622-0.00540.06911.4335-0.4049-0.99791.04670.11071.0113-59.1703-30.7129-46.167
270.471-0.192-0.62540.72120.50311.01430.14370.163-0.06790.0251-0.33310.0818-0.4942-0.36260.25551.2521-0.076-0.30610.545-0.03930.5022-44.825-29.0973-40.5559
280.30790.0837-0.26930.1545-0.05840.9703-0.0426-0.2574-0.332-0.104-0.3815-0.0886-0.629-0.26730.30081.39250.0338-0.4960.4892-0.13960.3771-39.337-26.6895-46.0346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 47:66)A47 - 66
2X-RAY DIFFRACTION2(chain A and resid 67:104)A67 - 104
3X-RAY DIFFRACTION3(chain A and resid 105:115)A105 - 115
4X-RAY DIFFRACTION4(chain A and resid 116:138)A116 - 138
5X-RAY DIFFRACTION5(chain A and resid 139:158)A139 - 158
6X-RAY DIFFRACTION6(chain A and resid 159:164)A159 - 164
7X-RAY DIFFRACTION7(chain A and resid 165:187)A165 - 187
8X-RAY DIFFRACTION8(chain A and resid 188:236)A188 - 236
9X-RAY DIFFRACTION9(chain A and resid 237:301)A237 - 301
10X-RAY DIFFRACTION10(chain A and resid 302:321)A302 - 321
11X-RAY DIFFRACTION11(chain A and resid 322:337)A322 - 337
12X-RAY DIFFRACTION12(chain A and resid 338:356)A338 - 356
13X-RAY DIFFRACTION13(chain A and resid 357:395)A357 - 395
14X-RAY DIFFRACTION14(chain B and resid 14:18)B14 - 18
15X-RAY DIFFRACTION15(chain B and resid 19:37)B19 - 37
16X-RAY DIFFRACTION16(chain B and resid 38:52)B38 - 52
17X-RAY DIFFRACTION17(chain B and resid 53:67)B53 - 67
18X-RAY DIFFRACTION18(chain B and resid 68:75)B68 - 75
19X-RAY DIFFRACTION19(chain B and resid 76:88)B76 - 88
20X-RAY DIFFRACTION20(chain B and resid 89:95)B89 - 95
21X-RAY DIFFRACTION21(chain B and resid 96:105)B96 - 105
22X-RAY DIFFRACTION22(chain B and resid 106:113)B106 - 113
23X-RAY DIFFRACTION23(chain B and resid 114:123)B114 - 123
24X-RAY DIFFRACTION24(chain B and resid 124:131)B124 - 131
25X-RAY DIFFRACTION25(chain B and resid 132:138)B132 - 138
26X-RAY DIFFRACTION26(chain B and resid 139:146)B139 - 146
27X-RAY DIFFRACTION27(chain B and resid 147:159)B147 - 159
28X-RAY DIFFRACTION28(chain B and resid 160:173)B160 - 173

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